From b23b46af0e3e8e23fabafbccbc1b6f8662b54450 Mon Sep 17 00:00:00 2001 From: Bartosz Bosak Date: Fri, 2 Dec 2022 13:36:02 +0100 Subject: [PATCH 01/42] added reference to QCG-PJ parallel tasks template --- easyvvuq/actions/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easyvvuq/actions/__init__.py b/easyvvuq/actions/__init__.py index d98792834..a076e0176 100644 --- a/easyvvuq/actions/__init__.py +++ b/easyvvuq/actions/__init__.py @@ -8,7 +8,7 @@ from .execute_local import ExecuteLocal, ExecutePython, CreateRunDirectory, Encode, Decode, local_execute from .execute_local import CleanUp, Actions -from .execute_qcgpj import QCGPJPool, EasyVVUQBasicTemplate, ExecuteQCGPJ +from .execute_qcgpj import QCGPJPool, EasyVVUQBasicTemplate, EasyVVUQParallelTemplate from .execute_kubernetes import ExecuteKubernetes from .execute_slurm import ExecuteSLURM from .action_statuses import ActionPool From a24173aaf3b40ee18ea8d51251f48189395ba95c Mon Sep 17 00:00:00 2001 From: Bartosz Bosak Date: Wed, 7 Dec 2022 11:50:55 +0100 Subject: [PATCH 02/42] returning ndarray instead of scalar value --- easyvvuq/analysis/pce_analysis.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easyvvuq/analysis/pce_analysis.py b/easyvvuq/analysis/pce_analysis.py index e73579a6f..572ac2702 100644 --- a/easyvvuq/analysis/pce_analysis.py +++ b/easyvvuq/analysis/pce_analysis.py @@ -108,15 +108,15 @@ def _describe(self, qoi, statistic): return np.array([v.upper[0] for _, v in enumerate( self.raw_data['output_distributions'][qoi])]) elif statistic == '1%': - return self.raw_data['percentiles'][qoi]['p01'] + return np.array([self.raw_data['percentiles'][qoi]['p01']]) elif statistic == '10%': - return self.raw_data['percentiles'][qoi]['p10'] + return np.array([self.raw_data['percentiles'][qoi]['p10']]) elif statistic == '90%': - return self.raw_data['percentiles'][qoi]['p90'] + return np.array([self.raw_data['percentiles'][qoi]['p90']]) elif statistic == '99%': - return self.raw_data['percentiles'][qoi]['p99'] + return np.array([self.raw_data['percentiles'][qoi]['p99']]) elif statistic == 'median': - return self.raw_data['percentiles'][qoi]['p50'] + return np.array([self.raw_data['percentiles'][qoi]['p50']]) else: try: return self.raw_data['statistical_moments'][qoi][statistic] From 75c411d3400a921cb6027d4eece74e52f7920d10 Mon Sep 17 00:00:00 2001 From: Bartosz Bosak Date: Wed, 7 Dec 2022 13:32:20 +0100 Subject: [PATCH 03/42] fix for vector qois --- easyvvuq/analysis/pce_analysis.py | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/easyvvuq/analysis/pce_analysis.py b/easyvvuq/analysis/pce_analysis.py index 572ac2702..85ea70f84 100644 --- a/easyvvuq/analysis/pce_analysis.py +++ b/easyvvuq/analysis/pce_analysis.py @@ -108,15 +108,30 @@ def _describe(self, qoi, statistic): return np.array([v.upper[0] for _, v in enumerate( self.raw_data['output_distributions'][qoi])]) elif statistic == '1%': - return np.array([self.raw_data['percentiles'][qoi]['p01']]) + if isinstance(self.raw_data['percentiles'][qoi]['p01'], np.ndarray): + return self.raw_data['percentiles'][qoi]['p01'] + else: + return np.array([self.raw_data['percentiles'][qoi]['p01']]) elif statistic == '10%': - return np.array([self.raw_data['percentiles'][qoi]['p10']]) + if isinstance(self.raw_data['percentiles'][qoi]['p10'], np.ndarray): + return self.raw_data['percentiles'][qoi]['p10'] + else: + return np.array([self.raw_data['percentiles'][qoi]['p10']]) elif statistic == '90%': - return np.array([self.raw_data['percentiles'][qoi]['p90']]) + if isinstance(self.raw_data['percentiles'][qoi]['p90'], np.ndarray): + return self.raw_data['percentiles'][qoi]['p90'] + else: + return np.array([self.raw_data['percentiles'][qoi]['p90']]) elif statistic == '99%': - return np.array([self.raw_data['percentiles'][qoi]['p99']]) + if isinstance(self.raw_data['percentiles'][qoi]['p99'], np.ndarray): + return self.raw_data['percentiles'][qoi]['p99'] + else: + return np.array([self.raw_data['percentiles'][qoi]['p99']]) elif statistic == 'median': - return np.array([self.raw_data['percentiles'][qoi]['p50']]) + if isinstance(self.raw_data['percentiles'][qoi]['p50'], np.ndarray): + return self.raw_data['percentiles'][qoi]['p50'] + else: + return np.array([self.raw_data['percentiles'][qoi]['p50']]) else: try: return self.raw_data['statistical_moments'][qoi][statistic] From 58a213fcc4287eb57cbb1bee9eeb7882341d0781 Mon Sep 17 00:00:00 2001 From: Bartosz Bosak Date: Wed, 11 Jan 2023 10:50:01 +0100 Subject: [PATCH 04/42] remove plotting of 1% and 99% qois when they don't exist --- easyvvuq/analysis/results.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easyvvuq/analysis/results.py b/easyvvuq/analysis/results.py index 98bb5024b..f9e3b8903 100644 --- a/easyvvuq/analysis/results.py +++ b/easyvvuq/analysis/results.py @@ -546,8 +546,9 @@ def plot_moments( self.describe(qoi, 'std'), self.describe(qoi, 'mean') + self.describe(qoi, 'std'), label='std', alpha=alpha) ax.plot(xvalues, self.describe(qoi, 'mean'), label='mean') - ax.plot(xvalues, self.describe(qoi, '1%'), '--', label='1%', color='black') - ax.plot(xvalues, self.describe(qoi, '99%'), '--', label='99%', color='black') + if all(v in self.supported_stats() for v in ['1%', '99%']): + ax.plot(xvalues, self.describe(qoi, '1%'), '--', label='1%', color='black') + ax.plot(xvalues, self.describe(qoi, '99%'), '--', label='99%', color='black') ax.grid(True) if ylabel is None: ax.set_ylabel(qoi) From 930ff25151c4e01b289259fc930943c7e6447254 Mon Sep 17 00:00:00 2001 From: Jon McCullough Date: Tue, 5 Dec 2023 14:15:37 +0000 Subject: [PATCH 05/42] Modify test_anisotropic_order to prevent warning message --- tests/test_anisotropic_order.py | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/tests/test_anisotropic_order.py b/tests/test_anisotropic_order.py index 9c0fa972e..5650e902e 100644 --- a/tests/test_anisotropic_order.py +++ b/tests/test_anisotropic_order.py @@ -71,14 +71,7 @@ def test_anisotropic_order(tmpdir): my_campaign.apply_analysis(analysis) results = my_campaign.get_last_analysis() - - return results, sampler, analysis - - -if __name__ == "__main__": - - results, sampler, analysis = test_anisotropic_order("/tmp") - + ################################### # Plot the moments and SC samples # ################################### @@ -136,6 +129,7 @@ def test_anisotropic_order(tmpdir): leg.set_draggable(True) plt.tight_layout() + plt.savefig('/tmp/test_anisotropic_order_sobols.png') ############# # Plot grid # @@ -144,3 +138,8 @@ def test_anisotropic_order(tmpdir): analysis.plot_grid() # plt.show() + +if __name__ == "__main__": + + test_anisotropic_order("/tmp") + From 1639bb92a97fb368e3a7f2d2542684346c23cbcf Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:02:13 +0100 Subject: [PATCH 06/42] Update codeql.yml to v3 #424 --- .github/workflows/codeql.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 01ef0cc5e..9986b52f0 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -27,15 +27,15 @@ jobs: uses: actions/checkout@v3 - name: Initialize CodeQL - uses: github/codeql-action/init@v2 + uses: github/codeql-action/init@v3 with: languages: ${{ matrix.language }} queries: +security-and-quality - name: Autobuild - uses: github/codeql-action/autobuild@v2 + uses: github/codeql-action/autobuild@v3 - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v2 + uses: github/codeql-action/analyze@v3 with: category: "/language:${{ matrix.language }}" From 6007dbc67dde8e80648bf8ffa39556812e994d03 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:03:50 +0100 Subject: [PATCH 07/42] Update benchmark.yml actions --- .github/workflows/benchmark.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index ab7ac7d13..13c57bfd2 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -15,9 +15,9 @@ jobs: python-version: ['3.10'] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v3 with: python-version: ${{ matrix.python-version }} - name: Install dependencies From 8c73ce42b5de23ee35589bd8b100b13f7ccb597c Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:04:11 +0100 Subject: [PATCH 08/42] Update coveralls.yml --- .github/workflows/coveralls.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/coveralls.yml b/.github/workflows/coveralls.yml index 5050dff31..479657b5c 100644 --- a/.github/workflows/coveralls.yml +++ b/.github/workflows/coveralls.yml @@ -18,9 +18,9 @@ jobs: python-version: ['3.10'] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v3 with: python-version: ${{ matrix.python-version }} - name: Install dependencies From cd1ed3884b0ffc52b6921856cb5649aa60022ba8 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:04:27 +0100 Subject: [PATCH 09/42] Update docker.yml --- .github/workflows/docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 705d7f6e5..54a236202 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -6,7 +6,7 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Copy Dockerfile run: | cp tutorials/kubernetes/Dockerfile . From a849507be353b83468abfcf4bc2238bed59206f5 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:05:03 +0100 Subject: [PATCH 10/42] Update pdocs.yml --- .github/workflows/pdocs.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pdocs.yml b/.github/workflows/pdocs.yml index 345183ceb..17b058e50 100644 --- a/.github/workflows/pdocs.yml +++ b/.github/workflows/pdocs.yml @@ -13,9 +13,9 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v3 with: python-version: '3.x' - name: Install dependencies @@ -26,7 +26,7 @@ jobs: cd tests/cannonsim/src; make; cd ../../.. pip install pdoc - name: Checkout - uses: actions/checkout@v2.3.1 + uses: actions/checkout@v3 - name: Build run: | export PDOC_ALLOW_EXEC=1 From 06f8fd404801c83c6afa184e7c650237a80df06c Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:05:24 +0100 Subject: [PATCH 11/42] Update python-package.yml --- .github/workflows/python-package.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 331adc678..f3bcb3ecf 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -18,9 +18,9 @@ jobs: python-version: ['3.8', '3.9', '3.10', '3.11'] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v3 with: python-version: ${{ matrix.python-version }} - name: Install dependencies From 1f6592088514aed2faeedb17d3e43237479ad076 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:05:40 +0100 Subject: [PATCH 12/42] Update pythonpublish.yml --- .github/workflows/pythonpublish.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pythonpublish.yml b/.github/workflows/pythonpublish.yml index 4e1ef42d2..0ae487562 100644 --- a/.github/workflows/pythonpublish.yml +++ b/.github/workflows/pythonpublish.yml @@ -13,9 +13,9 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v3 with: python-version: '3.x' - name: Install dependencies From f06e892d2521b88c319e9ba433e96559957159c3 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:11:43 +0100 Subject: [PATCH 13/42] Update benchmark.yml --- .github/workflows/benchmark.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 13c57bfd2..767b7ccf9 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -15,7 +15,7 @@ jobs: python-version: ['3.10'] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v3 with: From 2fd0f9727c7bce1503249612dc66fa0b44883133 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:11:57 +0100 Subject: [PATCH 14/42] Update codeql.yml --- .github/workflows/codeql.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 9986b52f0..e6f393ac6 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -24,7 +24,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Initialize CodeQL uses: github/codeql-action/init@v3 From 38c25e22c8c7640e7d861f514953302120f59560 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:12:10 +0100 Subject: [PATCH 15/42] Update coveralls.yml --- .github/workflows/coveralls.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/coveralls.yml b/.github/workflows/coveralls.yml index 479657b5c..abfd2b1fe 100644 --- a/.github/workflows/coveralls.yml +++ b/.github/workflows/coveralls.yml @@ -18,7 +18,7 @@ jobs: python-version: ['3.10'] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v3 with: From c344fd2b1bd1d5ce452f0d91185bfcc451e0facd Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:12:23 +0100 Subject: [PATCH 16/42] Update docker.yml --- .github/workflows/docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 54a236202..13a511e91 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -6,7 +6,7 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Copy Dockerfile run: | cp tutorials/kubernetes/Dockerfile . From 45bae67e66582b99e9f27f13a10b5a88ed67213c Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:12:36 +0100 Subject: [PATCH 17/42] Update pdocs.yml --- .github/workflows/pdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pdocs.yml b/.github/workflows/pdocs.yml index 17b058e50..41c02641a 100644 --- a/.github/workflows/pdocs.yml +++ b/.github/workflows/pdocs.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v3 with: From 6d92d361da289a48ce8b32efd9b009e08a5d8248 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:12:48 +0100 Subject: [PATCH 18/42] Update python-package.yml --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index f3bcb3ecf..2ef626b85 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -18,7 +18,7 @@ jobs: python-version: ['3.8', '3.9', '3.10', '3.11'] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v3 with: From f91fc4e2fea97a9fba5e2e33aae14944ab261516 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:12:59 +0100 Subject: [PATCH 19/42] Update pythonpublish.yml --- .github/workflows/pythonpublish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonpublish.yml b/.github/workflows/pythonpublish.yml index 0ae487562..dc32c7270 100644 --- a/.github/workflows/pythonpublish.yml +++ b/.github/workflows/pythonpublish.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v3 with: From e3648cd8bd047e155de1f4ee780fac4535a210eb Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:31:36 +0100 Subject: [PATCH 20/42] Update benchmark.yml --- .github/workflows/benchmark.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 767b7ccf9..f8bc08d1d 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -17,7 +17,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - name: Install dependencies From 4abbf6c5fd5433cb136c7e211833c5bd01779695 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:32:08 +0100 Subject: [PATCH 21/42] Update coveralls.yml --- .github/workflows/coveralls.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/coveralls.yml b/.github/workflows/coveralls.yml index abfd2b1fe..430078749 100644 --- a/.github/workflows/coveralls.yml +++ b/.github/workflows/coveralls.yml @@ -20,7 +20,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - name: Install dependencies From bc4ae8e4c3409a1dc39daf6f574ce03e12be0c1a Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:32:32 +0100 Subject: [PATCH 22/42] Update pdocs.yml --- .github/workflows/pdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pdocs.yml b/.github/workflows/pdocs.yml index 41c02641a..ff37bcc36 100644 --- a/.github/workflows/pdocs.yml +++ b/.github/workflows/pdocs.yml @@ -15,7 +15,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v3 + uses: actions/setup-python@v4 with: python-version: '3.x' - name: Install dependencies From 39ef8e55a3531fc334acf16935b4c5ffeca1268f Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:32:44 +0100 Subject: [PATCH 23/42] Update python-package.yml --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 2ef626b85..29d7bec5d 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -20,7 +20,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - name: Install dependencies From ca80168307e8570030dcf340fb8024712bc2c5b8 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:32:56 +0100 Subject: [PATCH 24/42] Update pythonpublish.yml --- .github/workflows/pythonpublish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonpublish.yml b/.github/workflows/pythonpublish.yml index dc32c7270..16b7f207d 100644 --- a/.github/workflows/pythonpublish.yml +++ b/.github/workflows/pythonpublish.yml @@ -15,7 +15,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v3 + uses: actions/setup-python@v4 with: python-version: '3.x' - name: Install dependencies From e85dedda2ea1466fbf986a361b242dde073d6e9c Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 17 Jul 2024 11:46:52 +0100 Subject: [PATCH 25/42] Updated setup-python action to v5. --- .github/workflows/benchmark.yml | 2 +- .github/workflows/coveralls.yml | 2 +- .github/workflows/pdocs.yml | 2 +- .github/workflows/python-package.yml | 2 +- .github/workflows/pythonpublish.yml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index f8bc08d1d..97ae3c935 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -17,7 +17,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies diff --git a/.github/workflows/coveralls.yml b/.github/workflows/coveralls.yml index 430078749..cb17ff93e 100644 --- a/.github/workflows/coveralls.yml +++ b/.github/workflows/coveralls.yml @@ -20,7 +20,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies diff --git a/.github/workflows/pdocs.yml b/.github/workflows/pdocs.yml index ff37bcc36..e770172aa 100644 --- a/.github/workflows/pdocs.yml +++ b/.github/workflows/pdocs.yml @@ -15,7 +15,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.x' - name: Install dependencies diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 29d7bec5d..f5022fb20 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -20,7 +20,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies diff --git a/.github/workflows/pythonpublish.yml b/.github/workflows/pythonpublish.yml index 16b7f207d..ce25ff78e 100644 --- a/.github/workflows/pythonpublish.yml +++ b/.github/workflows/pythonpublish.yml @@ -15,7 +15,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.x' - name: Install dependencies From 0a5867e9b084e851e78d75eda41abc6c988868c6 Mon Sep 17 00:00:00 2001 From: Bartosz Bosak Date: Mon, 22 Jul 2024 11:19:41 +0200 Subject: [PATCH 26/42] added suppport for modules in QCG-PJ templates --- easyvvuq/actions/execute_qcgpj.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easyvvuq/actions/execute_qcgpj.py b/easyvvuq/actions/execute_qcgpj.py index 03db3ae4d..467bdd205 100644 --- a/easyvvuq/actions/execute_qcgpj.py +++ b/easyvvuq/actions/execute_qcgpj.py @@ -37,6 +37,7 @@ def template() -> Tuple[str, Dict[str, Any]]: 'stdout': '${stdout}', 'stderr': '${stderr}', 'venv': '${venv}', + 'modules': ${modules}, 'model': '${model}', 'model_opts': ${model_opts} } @@ -48,6 +49,7 @@ def template() -> Tuple[str, Dict[str, Any]]: 'stdout': 'stdout', 'stderr': 'stderr', 'venv': '', + 'modules': [], 'model': 'default', 'model_opts': {} } @@ -74,6 +76,7 @@ def template() -> Tuple[str, Dict[str, Any]]: 'stdout': '${stdout}', 'stderr': '${stderr}', 'venv': '${venv}', + 'modules': ${modules}, 'model': '${model}', 'model_opts': ${model_opts} }, @@ -93,6 +96,7 @@ def template() -> Tuple[str, Dict[str, Any]]: 'stdout': 'stdout', 'stderr': 'stderr', 'venv': '', + 'modules': [], 'model': 'default', 'model_opts': {}, 'numCores': 1, From 910ad8a4aeb993affdca2c4618aa96ebaee75cce Mon Sep 17 00:00:00 2001 From: Bartosz Bosak Date: Mon, 22 Jul 2024 12:10:01 +0200 Subject: [PATCH 27/42] Added EnsebleBootMultiple class to enable analysis of many statistics at once. --- easyvvuq/analysis/__init__.py | 2 +- easyvvuq/analysis/ensemble_boot.py | 93 ++++++++++++++++++++++++++++++ 2 files changed, 94 insertions(+), 1 deletion(-) diff --git a/easyvvuq/analysis/__init__.py b/easyvvuq/analysis/__init__.py index 8694a0bf1..181949133 100644 --- a/easyvvuq/analysis/__init__.py +++ b/easyvvuq/analysis/__init__.py @@ -1,5 +1,5 @@ from .basic_stats import BasicStats -from .ensemble_boot import EnsembleBoot +from .ensemble_boot import EnsembleBoot, EnsembleBootMultiple from .sc_analysis import SCAnalysis from .ssc_analysis import SSCAnalysis from .pce_analysis import PCEAnalysis diff --git a/easyvvuq/analysis/ensemble_boot.py b/easyvvuq/analysis/ensemble_boot.py index 35ba01160..c30699c62 100644 --- a/easyvvuq/analysis/ensemble_boot.py +++ b/easyvvuq/analysis/ensemble_boot.py @@ -289,3 +289,96 @@ def analyse(self, data_frame=None): stat_name=self.stat_name) return results + +class EnsembleBootMultiple(BaseAnalysisElement): + + def __init__(self, groupby=[], qoi_cols=[], + stat_func=[np.mean], alpha=0.05, + sample_size=None, n_boot_samples=1000, + pivotal=False, stat_name=None): + """ + Element to perform bootstrapping on collated simulation output. + + Parameters + ---------- + groupby : list or None + Columns to use to group the data in `analyse` method before + calculating stats. + qoi_cols : list or None + Columns of quantities of interest (for which stats will be + calculated). + stat_func : list[function] + List of statistical functions to be applied to data for bootstrapping. + alpha : float, default=0.05 + Produce estimate of 100.0*(1-`alpha`) confidence interval. + sample_size : int + Size of the sample to be drawn from the input data. + n_boot_samples : int, default=1000 + Number of times samples are to be drawn from the input data. + pivotal : bool, default=False + Use the pivotal method? Default to percentile method. + stat_name : str, default=None + Name to use to describe columns containing output statistic (for example + 'mean'). If not provided, then attr '__name__' from each func is used. + """ + + if not stat_func or stat_func is None: + raise ValueError('stat_func cannot be empty or None') + + self.groupby = groupby + self.qoi_cols = qoi_cols + + self.stat_func = stat_func + self.alpha = alpha + self.sample_size = sample_size + self.n_boot_samples = n_boot_samples + self.pivotal = pivotal + self.stat_name = stat_name if stat_name is not None else [func.__name__ for func in stat_func] + + self.output_type = OutputType.SUMMARY + + def element_name(self): + """Name for this element for logging purposes""" + return "ensemble_boot" + + def element_version(self): + """Version of this element for logging purposes""" + return "0.1" + + def analyse(self, data_frame=None): + """Perform bootstrapping analysis on the input `data_frame`. + + The data_frame is grouped according to `self.groupby` if specified and + analysis is performed on the columns selected in `self.qoi_cols` if set. + + Parameters + ---------- + data_frame : :obj:`pandas.DataFrame` + Summary data produced through collation of simulation output. + + Returns + ------- + :obj:`pandas.DataFrame` + Basic statistic for selected columns and groupings of data. + """ + + if data_frame is None: + raise RuntimeError( + "This VVUQ element needs a data frame to analyse") + elif data_frame.empty: + raise RuntimeError( + "No data in data frame passed to analyse element") + frames = [] + for stat_func, stat_name in zip(self.stat_func, self.stat_name): + results = ensemble_bootstrap( + data_frame, + groupby=self.groupby, + qoi_cols=self.qoi_cols, + stat_func=stat_func, + alpha=self.alpha, + sample_size=self.sample_size, + n_samples=self.n_boot_samples, + pivotal=self.pivotal, + stat_name=stat_name) + frames.append(results) + return pd.concat(frames, axis=1, keys=self.stat_name).swaplevel(0, 1, axis=1) From 6aee7a60f77063faedb54820ce8f41cea0efcd3c Mon Sep 17 00:00:00 2001 From: Bartosz Bosak Date: Wed, 19 Jun 2024 13:52:19 +0200 Subject: [PATCH 28/42] more stats for mc (cherry picked from commit d48cd025647ed9730e281592b3874863cda17b56) --- easyvvuq/analysis/qmc_analysis.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/easyvvuq/analysis/qmc_analysis.py b/easyvvuq/analysis/qmc_analysis.py index 328b07eea..45e2ff2d7 100644 --- a/easyvvuq/analysis/qmc_analysis.py +++ b/easyvvuq/analysis/qmc_analysis.py @@ -51,17 +51,21 @@ def supported_stats(self): ------- list of str """ - return ['mean', 'var', 'std', 'percentiles', '10%', '50%', '90%'] + return ['mean', 'var', 'std', 'min', 'max', 'median', 'percentiles', '1%', '10%', '50%', '90%', '99%'] def _describe(self, qoi, statistic): if statistic not in self.supported_stats(): raise NotImplementedError + if statistic == '1%': + return self.raw_data['percentiles'][qoi]['p1'] if statistic == '10%': return self.raw_data['percentiles'][qoi]['p10'] elif statistic == '50%': return self.raw_data['percentiles'][qoi]['p50'] elif statistic == '90%': return self.raw_data['percentiles'][qoi]['p90'] + elif statistic == '99%': + return self.raw_data['percentiles'][qoi]['p99'] else: return self.raw_data['statistical_moments'][qoi][statistic][0] @@ -206,10 +210,16 @@ def analyse(self, data_frame): results['statistical_moments'][k] = {'mean': np.mean(masked_samples, axis=0), 'var': np.var(masked_samples, axis=0), - 'std': np.std(masked_samples, axis=0)} - results['percentiles'][k] = {'p10': np.percentile(masked_samples, 10, 0)[0], + 'std': np.std(masked_samples, axis=0), + 'min': np.min(masked_samples, axis=0), + 'max': np.max(masked_samples, axis=0), + 'median': np.median(masked_samples, axis=0), + } + results['percentiles'][k] = {'p1': np.percentile(masked_samples, 1, 0)[0], + 'p10': np.percentile(masked_samples, 10, 0)[0], 'p50': np.percentile(masked_samples, 50, 0)[0], - 'p90': np.percentile(masked_samples, 90, 0)[0]} + 'p90': np.percentile(masked_samples, 90, 0)[0], + 'p99': np.percentile(masked_samples, 99, 0)[0]} # Replace Nan values by the mean before proceeding with the SA indices = np.where(mask == 0)[0] # samples[~mask] = results[k].mean From 03e5ea14d32dc3d8851788e8c009d36b4eba308c Mon Sep 17 00:00:00 2001 From: Bartosz Bosak Date: Mon, 22 Jul 2024 13:41:56 +0200 Subject: [PATCH 29/42] updated test to reflect new statistics --- tests/test_mc_analysis_results.py | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/tests/test_mc_analysis_results.py b/tests/test_mc_analysis_results.py index 09766bbf6..8c052d24f 100644 --- a/tests/test_mc_analysis_results.py +++ b/tests/test_mc_analysis_results.py @@ -119,18 +119,28 @@ def test_describe(results_vectors): results_vectors.describe()[ ('g', 1)].to_dict() == { + '1%': 0.007945053328978277, '10%': 0.08156520178597204, - '90%': 0.8729378821725343, + '90%': 0.8729378821725343, + '99%': 0.9950881374303691, + 'max': 0.9983981908285983, 'mean': 0.4691844466934421, - 'var': 0.08534945020531205, - 'std': 0.29214628220347433}) + 'median': 0.4495551186167759, + 'min': 0.0038532031638378594, + 'std': 0.29214628220347433, + 'var': 0.08534945020531205}) assert ( results_vectors.describe('h')[ ('h', 1)].to_dict() == { + '1%': 0.039851582820686876, '10%': 0.21724677702965456, '90%': 0.9764815719704141, + '99%': 0.9969701901368494, + 'max': 0.9993165378092128, 'mean': 0.6873389710989142, - 'var': 0.07501266456861228, - 'std': 0.27388440000958847}) + 'median': 0.7696583654805108, + 'min': 0.01590577381510083, + 'std': 0.27388440000958847, + 'var': 0.07501266456861228}) assert (isinstance(results_vectors.describe('h', 'std'), np.ndarray)) From c2b807cadcbf0c9f710bcb3488acfb15814f43ee Mon Sep 17 00:00:00 2001 From: Bartosz Bosak Date: Mon, 22 Jul 2024 14:09:13 +0200 Subject: [PATCH 30/42] added test for ensemble_boot_multiple --- tests/test_ensemble_boot.py | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/tests/test_ensemble_boot.py b/tests/test_ensemble_boot.py index b1592eb94..b656420a9 100644 --- a/tests/test_ensemble_boot.py +++ b/tests/test_ensemble_boot.py @@ -1,5 +1,5 @@ from easyvvuq.analysis.ensemble_boot import confidence_interval, bootstrap -from easyvvuq.analysis.ensemble_boot import ensemble_bootstrap, EnsembleBoot +from easyvvuq.analysis.ensemble_boot import ensemble_bootstrap, EnsembleBoot, EnsembleBootMultiple import os import numpy as np import pandas as pd @@ -82,3 +82,19 @@ def test_ensemble_boot(): 'b': ['group1'] * VALUES.shape[0] + ['group2'] * VALUES.shape[0]}) results = analysis.analyse(df) assert (not results.empty) + +def test_ensemble_boot_multiple(): + analysis = EnsembleBootMultiple() + assert (analysis.element_name() == 'ensemble_boot_multiple') + assert (analysis.element_version() == '0.1') + with pytest.raises(RuntimeError): + analysis.analyse() + with pytest.raises(RuntimeError): + analysis.analyse(pd.DataFrame({})) + analysis = EnsembleBootMultiple(groupby=['b'], qoi_cols=['a'], stat_func=[np.mean, np.var, np.median]) + df = pd.DataFrame({ + 'a': np.concatenate((VALUES, VALUES)), + 'b': ['group1'] * VALUES.shape[0] + ['group2'] * VALUES.shape[0]}) + results = analysis.analyse(df) + assert (not results.empty) + assert (results.values.shape == (2, 9)) From dd2915a667ce2a2a5a76ee85aaa70e23613cf39f Mon Sep 17 00:00:00 2001 From: Bartosz Bosak Date: Mon, 22 Jul 2024 14:18:19 +0200 Subject: [PATCH 31/42] updated name for ensemble_boot_multiple --- easyvvuq/analysis/ensemble_boot.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easyvvuq/analysis/ensemble_boot.py b/easyvvuq/analysis/ensemble_boot.py index c30699c62..202932086 100644 --- a/easyvvuq/analysis/ensemble_boot.py +++ b/easyvvuq/analysis/ensemble_boot.py @@ -339,7 +339,7 @@ def __init__(self, groupby=[], qoi_cols=[], def element_name(self): """Name for this element for logging purposes""" - return "ensemble_boot" + return "ensemble_boot_multiple" def element_version(self): """Version of this element for logging purposes""" From d421d71292615ae6757ea79eabd57df37db6c6ed Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 5 Aug 2024 11:15:05 +0100 Subject: [PATCH 32/42] Switch packaging to `pyproject.toml` Also requires switching auto-versioning to `setuptools_scm` from `versioneer`, as the latter doesn't work with `pyproject.toml`-only packages --- .gitignore | 1 + easyvvuq/__init__.py | 14 +- easyvvuq/_version.py | 683 ------------- install_EasyVVUQ.sh | 13 - pyproject.toml | 74 ++ requirements.txt | 29 - setup.cfg | 14 - setup.py | 41 - versioneer.py | 2277 ------------------------------------------ 9 files changed, 83 insertions(+), 3063 deletions(-) delete mode 100644 easyvvuq/_version.py delete mode 100644 install_EasyVVUQ.sh create mode 100644 pyproject.toml delete mode 100644 requirements.txt delete mode 100644 setup.cfg delete mode 100644 setup.py delete mode 100644 versioneer.py diff --git a/.gitignore b/.gitignore index 6f81966f1..e341b1a0d 100644 --- a/.gitignore +++ b/.gitignore @@ -21,3 +21,4 @@ pep.sh *.csv env/ .ipynb_checkpoints/ +easyvvuq/_version.py diff --git a/easyvvuq/__init__.py b/easyvvuq/__init__.py index 6ddc68ff9..d84419bf7 100644 --- a/easyvvuq/__init__.py +++ b/easyvvuq/__init__.py @@ -11,9 +11,14 @@ from . import analysis from . import comparison -# First make sure python version is 3.6+ -assert sys.version_info >= (3, 6), (f"Python version must be >= 3.6," - f"found {sys.version_info}") +from importlib.metadata import version, PackageNotFoundError + +try: + __version__ = version("easyvvuq") +except PackageNotFoundError: + from setuptools_scm import get_version # type: ignore[import] + + __version__ = get_version(root="..", relative_to=__file__) __copyright__ = """ @@ -36,6 +41,3 @@ """ __license__ = "LGPL" - -from . import _version -__version__ = _version.get_versions()['version'] diff --git a/easyvvuq/_version.py b/easyvvuq/_version.py deleted file mode 100644 index a89cb9e83..000000000 --- a/easyvvuq/_version.py +++ /dev/null @@ -1,683 +0,0 @@ - -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.29 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys -from typing import Any, Callable, Dict, List, Optional, Tuple -import functools - - -def get_keywords() -> Dict[str, str]: - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - VCS: str - style: str - tag_prefix: str - parentdir_prefix: str - versionfile_source: str - verbose: bool - - -def get_config() -> VersioneerConfig: - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440" - cfg.tag_prefix = "" - cfg.parentdir_prefix = "None" - cfg.versionfile_source = "easyvvuq/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f: Callable) -> Callable: - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command( - commands: List[str], - args: List[str], - cwd: Optional[str] = None, - verbose: bool = False, - hide_stderr: bool = False, - env: Optional[Dict[str, str]] = None, -) -> Tuple[Optional[str], Optional[int]]: - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs: Dict[str, Any] = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError as e: - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir( - parentdir_prefix: str, - root: str, - verbose: bool, -) -> Dict[str, Any]: - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords: Dict[str, str] = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords( - keywords: Dict[str, str], - tag_prefix: str, - verbose: bool, -) -> Dict[str, Any]: - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs( - tag_prefix: str, - root: str, - verbose: bool, - runner: Callable = run_command -) -> Dict[str, Any]: - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces: Dict[str, Any] = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces: Dict[str, Any]) -> str: - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces: Dict[str, Any]) -> str: - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces: Dict[str, Any]) -> str: - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces: Dict[str, Any]) -> str: - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces: Dict[str, Any]) -> str: - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces: Dict[str, Any]) -> str: - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions() -> Dict[str, Any]: - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} diff --git a/install_EasyVVUQ.sh b/install_EasyVVUQ.sh deleted file mode 100644 index b4cf56f9d..000000000 --- a/install_EasyVVUQ.sh +++ /dev/null @@ -1,13 +0,0 @@ -#1) Install Requirements -echo 'Install Requirements' -pip install -r requirements.txt - -#2) Install EasyVVUQ -echo 'Installing EasyVVUQ' -python -m pip install . - -#3) Build cannonsim test -echo 'Building cannonsim' -cd tests/cannonsim/src -make -cd ../../.. diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 000000000..9ac3c6aa4 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,74 @@ +[build-system] +requires = ["setuptools>=64", "setuptools_scm>=8"] +build-backend = "setuptools.build_meta" + +[project] +name = "easyvvuq" +description = "Library to facilitate simple Verification, Validation and Uncertainty Quantification of simulation codes" +readme = "README.md" +authors = [{name = "CCS"}] +license = {file = "LICENSE"} +dynamic = ["version"] +requires-python = ">=3.9" +dependencies = [ + "numpy<2", + "pandas", + "scipy", + "wheel", + "chaospy==4.3.2", + "numpoly==1.1.3", + "SALib", + "SQLAlchemy", + "cerberus", + "dask[complete]", + "dask_jobqueue", + "cloudpickle", + "scikit-learn", + "jinja2", + "kubernetes", + "squarify", + "dill", + "tqdm", + "qcg-pilotjob~=0.13.0", + "qcg-pilotjob-executor-api~=0.13.0", + "h5py", + "tomli", + "fipy", +] + +[project.optional-dependencies] +docs = [ + "sphinx >= 5.3", +] +tests = [ + "pytest >= 3.3.0", + "pytest-pep8", + "pytest-benchmark", + "pytest-dependency", +] +lint = [ + "black", + "ruff", +] + +[project.urls] +Source = "https://github.com/UCL-CCS/EasyVVUQ" +Tracker = "https://github.com/UCL-CCS/EasyVVUQ/issues" +Documentation = "https://easyvvuq.readthedocs.io/en/dev/" + +[tool.setuptools.packages.find] +where = ["easyvvuq"] + +[tool.setuptools_scm] +write_to = "easyvvuq/_version.py" + +[tool.black] +exclude = "easyvvuq/_version.py" + +[tool.pytest.ini_options] +pep8ignore = [ + "*.py E265", + "__init__.py E402", + "tests/*.py E128", +] +pep8maxlinelength = 100 diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 58437888e..000000000 --- a/requirements.txt +++ /dev/null @@ -1,29 +0,0 @@ -numpy<2 -pandas -scipy -wheel -chaospy==4.3.2 -numpoly==1.1.3 -SALib -pytest -pytest-pep8 -pytest-benchmark -pytest-dependency -SQLAlchemy -cerberus -dask[complete] -dask_jobqueue -cloudpickle -scikit-learn -jinja2 -kubernetes -autopep8 -squarify -dill -tqdm -qcg-pilotjob~=0.13.0 -qcg-pilotjob-executor-api~=0.13.0 -h5py -tomli -fipy -setuptools diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 7bab74efc..000000000 --- a/setup.cfg +++ /dev/null @@ -1,14 +0,0 @@ -[tool:pytest] -pep8ignore = - *.py E265 - __init__.py E402 - tests/*.py E128 -pep8maxlinelength=100 - -[versioneer] -# Automatic version numbering scheme -VCS = git -style = pep440 -versionfile_source = easyvvuq/_version.py -versionfile_build = easyvvuq/_version.py -tag_prefix = '' diff --git a/setup.py b/setup.py deleted file mode 100644 index 256de2933..000000000 --- a/setup.py +++ /dev/null @@ -1,41 +0,0 @@ -from os import path -import setuptools.command.build_py -from setuptools import setup, find_packages -import distutils -import versioneer -import subprocess - -class BuildPyCommand(setuptools.command.build_py.build_py): - def run(self): - setuptools.command.build_py.build_py.run(self) - -# read the contents of README file -this_directory = path.abspath(path.dirname(__file__)) -with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f: - long_description = f.read() - -cmdclass = versioneer.get_cmdclass() -cmdclass['build_py'] = BuildPyCommand - -setup( - name='easyvvuq', - - version=versioneer.get_version(), - cmdclass=cmdclass, - - description=('Library to facilitate simple Verification, Validation and ' - 'Uncertainty Quantification of simulation codes'), - - long_description=long_description, - long_description_content_type='text/markdown', - - url='https://readthedocs.org/projects/easyvvuq/', - - author='CCS', - - install_requires=open("requirements.txt", "r").readlines(), - - packages=find_packages(), - - include_package_data=True, -) diff --git a/versioneer.py b/versioneer.py deleted file mode 100644 index 1e3753e63..000000000 --- a/versioneer.py +++ /dev/null @@ -1,2277 +0,0 @@ - -# Version: 0.29 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/python-versioneer/python-versioneer -* Brian Warner -* License: Public Domain (Unlicense) -* Compatible with: Python 3.7, 3.8, 3.9, 3.10, 3.11 and pypy3 -* [![Latest Version][pypi-image]][pypi-url] -* [![Build Status][travis-image]][travis-url] - -This is a tool for managing a recorded version number in setuptools-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -Versioneer provides two installation modes. The "classic" vendored mode installs -a copy of versioneer into your repository. The experimental build-time dependency mode -is intended to allow you to skip this step and simplify the process of upgrading. - -### Vendored mode - -* `pip install versioneer` to somewhere in your $PATH - * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is - available, so you can also use `conda install -c conda-forge versioneer` -* add a `[tool.versioneer]` section to your `pyproject.toml` or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) - * Note that you will need to add `tomli; python_version < "3.11"` to your - build-time dependencies if you use `pyproject.toml` -* run `versioneer install --vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -### Build-time dependency mode - -* `pip install versioneer` to somewhere in your $PATH - * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is - available, so you can also use `conda install -c conda-forge versioneer` -* add a `[tool.versioneer]` section to your `pyproject.toml` or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) -* add `versioneer` (with `[toml]` extra, if configuring in `pyproject.toml`) - to the `requires` key of the `build-system` table in `pyproject.toml`: - ```toml - [build-system] - requires = ["setuptools", "versioneer[toml]"] - build-backend = "setuptools.build_meta" - ``` -* run `versioneer install --no-vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes). - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See [details.md](details.md) in the Versioneer -source tree for descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/python-versioneer/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other languages) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg` and `pyproject.toml`, if necessary, - to include any new configuration settings indicated by the release notes. - See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install --[no-]vendor` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - -## Similar projects - -* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time - dependency -* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of - versioneer -* [versioningit](https://github.com/jwodder/versioningit) - a PEP 518-based setuptools - plugin - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the "Unlicense", as described in -https://unlicense.org/. - -[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg -[pypi-url]: https://pypi.python.org/pypi/versioneer/ -[travis-image]: -https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg -[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer - -""" -# pylint:disable=invalid-name,import-outside-toplevel,missing-function-docstring -# pylint:disable=missing-class-docstring,too-many-branches,too-many-statements -# pylint:disable=raise-missing-from,too-many-lines,too-many-locals,import-error -# pylint:disable=too-few-public-methods,redefined-outer-name,consider-using-with -# pylint:disable=attribute-defined-outside-init,too-many-arguments - -import configparser -import errno -import json -import os -import re -import subprocess -import sys -from pathlib import Path -from typing import Any, Callable, cast, Dict, List, Optional, Tuple, Union -from typing import NoReturn -import functools - -have_tomllib = True -if sys.version_info >= (3, 11): - import tomllib -else: - try: - import tomli as tomllib - except ImportError: - have_tomllib = False - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - VCS: str - style: str - tag_prefix: str - versionfile_source: str - versionfile_build: Optional[str] - parentdir_prefix: Optional[str] - verbose: Optional[bool] - - -def get_root() -> str: - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - pyproject_toml = os.path.join(root, "pyproject.toml") - versioneer_py = os.path.join(root, "versioneer.py") - if not ( - os.path.exists(setup_py) - or os.path.exists(pyproject_toml) - or os.path.exists(versioneer_py) - ): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - pyproject_toml = os.path.join(root, "pyproject.toml") - versioneer_py = os.path.join(root, "versioneer.py") - if not ( - os.path.exists(setup_py) - or os.path.exists(pyproject_toml) - or os.path.exists(versioneer_py) - ): - err = ("Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND').") - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - my_path = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(my_path)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir and "VERSIONEER_PEP518" not in globals(): - print("Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(my_path), versioneer_py)) - except NameError: - pass - return root - - -def get_config_from_root(root: str) -> VersioneerConfig: - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise OSError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - root_pth = Path(root) - pyproject_toml = root_pth / "pyproject.toml" - setup_cfg = root_pth / "setup.cfg" - section: Union[Dict[str, Any], configparser.SectionProxy, None] = None - if pyproject_toml.exists() and have_tomllib: - try: - with open(pyproject_toml, 'rb') as fobj: - pp = tomllib.load(fobj) - section = pp['tool']['versioneer'] - except (tomllib.TOMLDecodeError, KeyError) as e: - print(f"Failed to load config from {pyproject_toml}: {e}") - print("Try to load it from setup.cfg") - if not section: - parser = configparser.ConfigParser() - with open(setup_cfg) as cfg_file: - parser.read_file(cfg_file) - parser.get("versioneer", "VCS") # raise error if missing - - section = parser["versioneer"] - - # `cast`` really shouldn't be used, but its simplest for the - # common VersioneerConfig users at the moment. We verify against - # `None` values elsewhere where it matters - - cfg = VersioneerConfig() - cfg.VCS = section['VCS'] - cfg.style = section.get("style", "") - cfg.versionfile_source = cast(str, section.get("versionfile_source")) - cfg.versionfile_build = section.get("versionfile_build") - cfg.tag_prefix = cast(str, section.get("tag_prefix")) - if cfg.tag_prefix in ("''", '""', None): - cfg.tag_prefix = "" - cfg.parentdir_prefix = section.get("parentdir_prefix") - if isinstance(section, configparser.SectionProxy): - # Make sure configparser translates to bool - cfg.verbose = section.getboolean("verbose") - else: - cfg.verbose = section.get("verbose") - - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f: Callable) -> Callable: - """Store f in HANDLERS[vcs][method].""" - HANDLERS.setdefault(vcs, {})[method] = f - return f - return decorate - - -def run_command( - commands: List[str], - args: List[str], - cwd: Optional[str] = None, - verbose: bool = False, - hide_stderr: bool = False, - env: Optional[Dict[str, str]] = None, -) -> Tuple[Optional[str], Optional[int]]: - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs: Dict[str, Any] = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError as e: - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -LONG_VERSION_PY['git'] = r''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.29 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys -from typing import Any, Callable, Dict, List, Optional, Tuple -import functools - - -def get_keywords() -> Dict[str, str]: - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - VCS: str - style: str - tag_prefix: str - parentdir_prefix: str - versionfile_source: str - verbose: bool - - -def get_config() -> VersioneerConfig: - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f: Callable) -> Callable: - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command( - commands: List[str], - args: List[str], - cwd: Optional[str] = None, - verbose: bool = False, - hide_stderr: bool = False, - env: Optional[Dict[str, str]] = None, -) -> Tuple[Optional[str], Optional[int]]: - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs: Dict[str, Any] = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError as e: - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir( - parentdir_prefix: str, - root: str, - verbose: bool, -) -> Dict[str, Any]: - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords: Dict[str, str] = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords( - keywords: Dict[str, str], - tag_prefix: str, - verbose: bool, -) -> Dict[str, Any]: - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs( - tag_prefix: str, - root: str, - verbose: bool, - runner: Callable = run_command -) -> Dict[str, Any]: - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces: Dict[str, Any] = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces: Dict[str, Any]) -> str: - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces: Dict[str, Any]) -> str: - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces: Dict[str, Any]) -> str: - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces: Dict[str, Any]) -> str: - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%%d.dev%%d" %% (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%%d" %% (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces: Dict[str, Any]) -> str: - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces: Dict[str, Any]) -> str: - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions() -> Dict[str, Any]: - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords: Dict[str, str] = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords( - keywords: Dict[str, str], - tag_prefix: str, - verbose: bool, -) -> Dict[str, Any]: - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs( - tag_prefix: str, - root: str, - verbose: bool, - runner: Callable = run_command -) -> Dict[str, Any]: - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces: Dict[str, Any] = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(versionfile_source: str, ipy: Optional[str]) -> None: - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [versionfile_source] - if ipy: - files.append(ipy) - if "VERSIONEER_PEP518" not in globals(): - try: - my_path = __file__ - if my_path.endswith((".pyc", ".pyo")): - my_path = os.path.splitext(my_path)[0] + ".py" - versioneer_file = os.path.relpath(my_path) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - with open(".gitattributes", "r") as fobj: - for line in fobj: - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - break - except OSError: - pass - if not present: - with open(".gitattributes", "a+") as fobj: - fobj.write(f"{versionfile_source} export-subst\n") - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir( - parentdir_prefix: str, - root: str, - verbose: bool, -) -> Dict[str, Any]: - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.29) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename: str) -> Dict[str, Any]: - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except OSError: - raise NotThisMethod("unable to read _version.py") - mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename: str, versions: Dict[str, Any]) -> None: - """Write the given version number to the given _version.py file.""" - contents = json.dumps(versions, sort_keys=True, - indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces: Dict[str, Any]) -> str: - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces: Dict[str, Any]) -> str: - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces: Dict[str, Any]) -> str: - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces: Dict[str, Any]) -> str: - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces: Dict[str, Any]) -> str: - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces: Dict[str, Any]) -> str: - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose: bool = False) -> Dict[str, Any]: - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or bool(cfg.verbose) # `bool()` used to avoid `None` - assert cfg.versionfile_source is not None, \ - "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, "error": "unable to compute version", - "date": None} - - -def get_version() -> str: - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(cmdclass: Optional[Dict[str, Any]] = None): - """Get the custom setuptools subclasses used by Versioneer. - - If the package uses a different cmdclass (e.g. one from numpy), it - should be provide as an argument. - """ - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/python-versioneer/python-versioneer/issues/52 - - cmds = {} if cmdclass is None else cmdclass.copy() - - # we add "version" to setuptools - from setuptools import Command - - class cmd_version(Command): - description = "report generated version string" - user_options: List[Tuple[str, str, str]] = [] - boolean_options: List[str] = [] - - def initialize_options(self) -> None: - pass - - def finalize_options(self) -> None: - pass - - def run(self) -> None: - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - cmds["version"] = cmd_version - - # we override "build_py" in setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # pip install -e . and setuptool/editable_wheel will invoke build_py - # but the build_py command is not expected to copy any files. - - # we override different "build_py" commands for both environments - if 'build_py' in cmds: - _build_py: Any = cmds['build_py'] - else: - from setuptools.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self) -> None: - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - if getattr(self, "editable_mode", False): - # During editable installs `.py` and data files are - # not copied to build_lib - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - cmds["build_py"] = cmd_build_py - - if 'build_ext' in cmds: - _build_ext: Any = cmds['build_ext'] - else: - from setuptools.command.build_ext import build_ext as _build_ext - - class cmd_build_ext(_build_ext): - def run(self) -> None: - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_ext.run(self) - if self.inplace: - # build_ext --inplace will only build extensions in - # build/lib<..> dir with no _version.py to write to. - # As in place builds will already have a _version.py - # in the module dir, we do not need to write one. - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if not cfg.versionfile_build: - return - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) - if not os.path.exists(target_versionfile): - print(f"Warning: {target_versionfile} does not exist, skipping " - "version update. This can happen if you are running build_ext " - "without first running build_py.") - return - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - cmds["build_ext"] = cmd_build_ext - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe # type: ignore - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self) -> None: - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if 'py2exe' in sys.modules: # py2exe enabled? - try: - from py2exe.setuptools_buildexe import py2exe as _py2exe # type: ignore - except ImportError: - from py2exe.distutils_buildexe import py2exe as _py2exe # type: ignore - - class cmd_py2exe(_py2exe): - def run(self) -> None: - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["py2exe"] = cmd_py2exe - - # sdist farms its file list building out to egg_info - if 'egg_info' in cmds: - _egg_info: Any = cmds['egg_info'] - else: - from setuptools.command.egg_info import egg_info as _egg_info - - class cmd_egg_info(_egg_info): - def find_sources(self) -> None: - # egg_info.find_sources builds the manifest list and writes it - # in one shot - super().find_sources() - - # Modify the filelist and normalize it - root = get_root() - cfg = get_config_from_root(root) - self.filelist.append('versioneer.py') - if cfg.versionfile_source: - # There are rare cases where versionfile_source might not be - # included by default, so we must be explicit - self.filelist.append(cfg.versionfile_source) - self.filelist.sort() - self.filelist.remove_duplicates() - - # The write method is hidden in the manifest_maker instance that - # generated the filelist and was thrown away - # We will instead replicate their final normalization (to unicode, - # and POSIX-style paths) - from setuptools import unicode_utils - normalized = [unicode_utils.filesys_decode(f).replace(os.sep, '/') - for f in self.filelist.files] - - manifest_filename = os.path.join(self.egg_info, 'SOURCES.txt') - with open(manifest_filename, 'w') as fobj: - fobj.write('\n'.join(normalized)) - - cmds['egg_info'] = cmd_egg_info - - # we override different "sdist" commands for both environments - if 'sdist' in cmds: - _sdist: Any = cmds['sdist'] - else: - from setuptools.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self) -> None: - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir: str, files: List[str]) -> None: - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, - self._versioneer_generated_versions) - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -OLD_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - -INIT_PY_SNIPPET = """ -from . import {0} -__version__ = {0}.get_versions()['version'] -""" - - -def do_setup() -> int: - """Do main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except (OSError, configparser.NoSectionError, - configparser.NoOptionError) as e: - if isinstance(e, (OSError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", - file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), - "__init__.py") - maybe_ipy: Optional[str] = ipy - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except OSError: - old = "" - module = os.path.splitext(os.path.basename(cfg.versionfile_source))[0] - snippet = INIT_PY_SNIPPET.format(module) - if OLD_SNIPPET in old: - print(" replacing boilerplate in %s" % ipy) - with open(ipy, "w") as f: - f.write(old.replace(OLD_SNIPPET, snippet)) - elif snippet not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(snippet) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - maybe_ipy = None - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(cfg.versionfile_source, maybe_ipy) - return 0 - - -def scan_setup_py() -> int: - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - - -def setup_command() -> NoReturn: - """Set up Versioneer and exit with appropriate error code.""" - errors = do_setup() - errors += scan_setup_py() - sys.exit(1 if errors else 0) - - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - setup_command() From 56e8b1823531637c46df9881482f9889a6643354 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 5 Aug 2024 11:31:52 +0100 Subject: [PATCH 33/42] Still support python 3.8 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9ac3c6aa4..75a3aa1cb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ readme = "README.md" authors = [{name = "CCS"}] license = {file = "LICENSE"} dynamic = ["version"] -requires-python = ">=3.9" +requires-python = ">=3.8" dependencies = [ "numpy<2", "pandas", From a5680ff2d59e867276ada059ec4be980711c9647 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 5 Aug 2024 11:41:09 +0100 Subject: [PATCH 34/42] Fix CI to use pyproject.toml --- .github/workflows/benchmark.yml | 9 +++------ .github/workflows/coveralls.yml | 9 ++++----- .github/workflows/pdocs.yml | 7 +++---- .github/workflows/python-package.yml | 9 ++++----- .github/workflows/pythonpublish.yml | 11 +++++++---- 5 files changed, 21 insertions(+), 24 deletions(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index ab7ac7d13..410aecbb4 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -15,18 +15,15 @@ jobs: python-version: ['3.10'] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - python setup.py develop - pip install pytest-benchmark + python -m pip install .[tests] - name: Benchmark with pytest run: | pytest tests/test_db_benchmark.py --benchmark-json output.json diff --git a/.github/workflows/coveralls.yml b/.github/workflows/coveralls.yml index 5050dff31..2093e968c 100644 --- a/.github/workflows/coveralls.yml +++ b/.github/workflows/coveralls.yml @@ -18,17 +18,16 @@ jobs: python-version: ['3.10'] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - python -m pip install --editable . + python -m pip install flake8 + python -m pip install --editable .[tests] cd tests/cannonsim/src; make; cd ../../.. pip install pytest-cov pip install coveralls diff --git a/.github/workflows/pdocs.yml b/.github/workflows/pdocs.yml index 345183ceb..a53ff79ec 100644 --- a/.github/workflows/pdocs.yml +++ b/.github/workflows/pdocs.yml @@ -13,16 +13,15 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: '3.x' - name: Install dependencies run: | python -m pip install --upgrade pip - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - python -m pip install --editable . + python -m pip install --editable .[docs] cd tests/cannonsim/src; make; cd ../../.. pip install pdoc - name: Checkout diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 331adc678..d230f244a 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -18,17 +18,16 @@ jobs: python-version: ['3.8', '3.9', '3.10', '3.11'] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - python -m pip install --editable . + python -m pip install flake8 + python -m pip install --editable .[tests] cd tests/cannonsim/src; make; cd ../../.. pip install pytest-cov pip install coveralls diff --git a/.github/workflows/pythonpublish.yml b/.github/workflows/pythonpublish.yml index 4e1ef42d2..349b2e2f6 100644 --- a/.github/workflows/pythonpublish.yml +++ b/.github/workflows/pythonpublish.yml @@ -13,19 +13,22 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: '3.x' - name: Install dependencies run: | python -m pip install --upgrade pip - pip install setuptools wheel twine + pip install build twine + - name: Build package + run: python -m build --sdist --wheel + - name: Check package + run: python -m twine check dist/* - name: Build and publish env: TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} run: | - python setup.py sdist bdist_wheel twine upload dist/* From 7f28323087fcda8f9079ee54a5f18c44f2b42c0a Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 5 Aug 2024 13:49:43 +0100 Subject: [PATCH 35/42] Docs: Install project on RTD --- .readthedocs.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 5fc242ca8..1befe0387 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -27,9 +27,9 @@ sphinx: # - pdf # - epub -# Optional but recommended, declare the Python requirements required -# to build your documentation -# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html -# python: -# install: -# - requirements: docs/requirements.txt \ No newline at end of file +python: + install: + - method: pip + path: . + extra_requirements: + - docs From 9523da25a903151939f238d7399eb3c0d02df60e Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 4 Dec 2024 10:45:35 +0000 Subject: [PATCH 36/42] Update pdocs.yml Attempt to fix docs build directly. --- .github/workflows/pdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pdocs.yml b/.github/workflows/pdocs.yml index f88958d62..c6bff6377 100644 --- a/.github/workflows/pdocs.yml +++ b/.github/workflows/pdocs.yml @@ -21,6 +21,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip + python -m pip install pkg_resources python -m pip install --editable .[docs] cd tests/cannonsim/src; make; cd ../../.. pip install pdoc From 02e00763f86b7f4dce149742733160d042dd951e Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 4 Dec 2024 10:46:38 +0000 Subject: [PATCH 37/42] Update pdocs.yml --- .github/workflows/pdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pdocs.yml b/.github/workflows/pdocs.yml index c6bff6377..9022b37c6 100644 --- a/.github/workflows/pdocs.yml +++ b/.github/workflows/pdocs.yml @@ -21,7 +21,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install pkg_resources + python -m pip install setuptools python -m pip install --editable .[docs] cd tests/cannonsim/src; make; cd ../../.. pip install pdoc From 8b775224a8fb5599c0b7aa46c717baabc3bfa170 Mon Sep 17 00:00:00 2001 From: David Coster Date: Wed, 4 Dec 2024 11:48:18 +0100 Subject: [PATCH 38/42] fix typo --- docs/source/concepts.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/concepts.rst b/docs/source/concepts.rst index 1afffa248..bca2cc9e4 100644 --- a/docs/source/concepts.rst +++ b/docs/source/concepts.rst @@ -140,4 +140,4 @@ Detailed information on the Analysis modules is available :doc:`here <_autodoc/e Execution --------- -Some more information on the use of QCG-Pilothob can be found :doc:`here `. +Some more information on the use of QCG-PilotJob can be found :doc:`here `. From 92ef364281dfa39056b031804ef5ab648aa81c2d Mon Sep 17 00:00:00 2001 From: Jon McCullough Date: Wed, 4 Dec 2024 11:01:34 +0000 Subject: [PATCH 39/42] Remove sc discrete uniform test - resolved with 402 and checked in another test --- tests/test_sc_discrete_uniform.py | 58 ------------------------------- 1 file changed, 58 deletions(-) delete mode 100644 tests/test_sc_discrete_uniform.py diff --git a/tests/test_sc_discrete_uniform.py b/tests/test_sc_discrete_uniform.py deleted file mode 100644 index 4eb10a668..000000000 --- a/tests/test_sc_discrete_uniform.py +++ /dev/null @@ -1,58 +0,0 @@ -import os -import numpy as np -import easyvvuq as uq -import chaospy as cp -from easyvvuq.actions import CreateRunDirectory, Encode, ExecuteLocal, Decode, Actions - -WORK_DIR = '/tmp' - -params = { - "steamT": {"type": "integer", "default": 600}, - "steamP": {"type": "integer", "default": 30}, - "liquidT": {"type": "float", "default": 10}, - "liquidP": {"type": "float", "default": 20}, - "liquidV": {"type": "integer", "default": 2}, - "tankV": {"type": "integer", "default": 15}, -} - -vary = { - "steamT": cp.DiscreteUniform(100, 600), - "steamP": cp.DiscreteUniform(5, 30), - "liquidT": cp.Normal(15, 3), - "liquidP": cp.Normal(10, 2), - "liquidV": cp.DiscreteUniform(1, 2), - # "tankV": cp.Normal(15, 2) # Tank V is const -} - -encoder = uq.encoders.GenericEncoder( - template_fname="./steam-water-equilibrium/config.template", delimiter="$", target_filename="input.json" -) - -decoder = uq.decoders.JSONDecoder( - target_filename="output.json", output_columns=["finalT", "finalP"] -) - -execute = ExecuteLocal(f"python3 {os.getcwd()}/steam-water-equilibrium/steam-water-equilibrium.py input.json") - -actions = Actions(CreateRunDirectory(WORK_DIR, flatten=True), - Encode(encoder), - execute, - Decode(decoder)) - -campaign = uq.Campaign(name="steam-water", params=params, actions=actions, - work_dir=WORK_DIR, verify_all_runs=True) - -### Sampler set -# sampler = uq.sampling.SCSampler(vary=vary, polynomial_order=1) -sampler = uq.sampling.PCESampler(vary=vary, polynomial_order=1) -campaign.set_sampler(sampler) - -# with QCGPJPool( -# template=EasyVVUQParallelTemplate(), -# template_params={ -# "venv": r"/home//.pyenv/versions/3.10.7/envs/steam-water" -# }, -# ) as qcgpj: -# campaign.execute(pool=qcgpj).collate() - -campaign.execute().collate() From 9d5aa18a48f11d527d3267d9fa3612ceb98ca37e Mon Sep 17 00:00:00 2001 From: mzrghorbani Date: Wed, 4 Dec 2024 12:41:27 +0000 Subject: [PATCH 40/42] Fix issue #391 with database dump. --- easyvvuq/db/sql.py | 13 +++++- tutorials/basic_tutorial_qcgpj.py | 75 ++++++++++++++++++++----------- 2 files changed, 60 insertions(+), 28 deletions(-) diff --git a/easyvvuq/db/sql.py b/easyvvuq/db/sql.py index 7c07d10bf..8ee7dc2e7 100644 --- a/easyvvuq/db/sql.py +++ b/easyvvuq/db/sql.py @@ -948,6 +948,15 @@ def dump(self): meta = MetaData() meta.reflect(bind=self.engine) result = {} - for table in meta.sorted_tables: - result[table.name] = [dict(row) for row in self.engine.execute(table.select())] + + # Create a connection from the engine + with self.engine.connect() as connection: + for table in meta.sorted_tables: + try: + query_result = connection.execute(table.select()).fetchall() + result[table.name] = [dict(row) for row in query_result] + except Exception as e: + result[table.name] = str(e) + return json.dumps(result) + diff --git a/tutorials/basic_tutorial_qcgpj.py b/tutorials/basic_tutorial_qcgpj.py index 5cd794675..147d36c80 100644 --- a/tutorials/basic_tutorial_qcgpj.py +++ b/tutorials/basic_tutorial_qcgpj.py @@ -3,52 +3,75 @@ import chaospy as cp import matplotlib.pyplot as plt +# Import necessary actions from EasyVVUQ from easyvvuq.actions import QCGPJPool from easyvvuq.actions import CreateRunDirectory, Encode, Decode, ExecuteLocal, Actions +# Define the parameters for the model params = { - "F": {"type": "float", "default": 1.0}, - "L": {"type": "float", "default": 1.5}, - "a": {"type": "float", "min": 0.7, "max": 1.2, "default": 1.0}, - "D": {"type": "float", "min": 0.75, "max": 0.85, "default": 0.8}, - "d": {"type": "float", "default": 0.1}, - "E": {"type": "float", "default": 200000}, - "outfile": {"type": "string", "default": "output.json"} + "F": {"type": "float", "default": 1.0}, # Force parameter + "L": {"type": "float", "default": 1.5}, # Length parameter + "a": {"type": "float", "min": 0.7, "max": 1.2, "default": 1.0}, # Variable a with range + "D": {"type": "float", "min": 0.75, "max": 0.85, "default": 0.8}, # Variable D with range + "d": {"type": "float", "default": 0.1}, # Variable d + "E": {"type": "float", "default": 200000}, # Young's modulus (material property) + "outfile": {"type": "string", "default": "output.json"} # Output file name } -encoder = uq.encoders.GenericEncoder(template_fname='beam.template', delimiter='$', target_filename='input.json') -decoder = uq.decoders.JSONDecoder(target_filename='output.json', output_columns=['g1']) -execute = ExecuteLocal('{}/beam input.json'.format(os.getcwd())) +# Set up the encoder and decoder to read/write data +encoder = uq.encoders.GenericEncoder(template_fname='beam.template', delimiter='$', target_filename='input.json') # Template encoder +decoder = uq.decoders.JSONDecoder(target_filename='output.json', output_columns=['g1']) # Decoder to read the output 'g1' -actions = Actions(CreateRunDirectory('/tmp'), - Encode(encoder), execute, Decode(decoder)) +# Execute the local model using the 'beam' input file +execute = ExecuteLocal('{}/beam input.json'.format(os.getcwd())) # Path to the model script and input file +# Set up the actions for the campaign +actions = Actions( + CreateRunDirectory('/tmp'), # Create a directory to store results + Encode(encoder), # Encode the input data + execute, # Run the computational model + Decode(decoder) # Decode the results from the output +) +# Create the EasyVVUQ campaign using the parameters and actions defined above campaign = uq.Campaign(name='beam', params=params, actions=actions) +# Define the uncertainty distributions for the input parameters using Chaospy vary = { - "F": cp.Normal(1, 0.1), - "L": cp.Normal(1.5, 0.01), - "a": cp.Uniform(0.7, 1.2), - "D": cp.Triangle(0.75, 0.8, 0.85) + "F": cp.Normal(1, 0.1), # Normal distribution for Force with mean 1 and std 0.1 + "L": cp.Normal(1.5, 0.01), # Normal distribution for Length with mean 1.5 and std 0.01 + "a": cp.Uniform(0.7, 1.2), # Uniform distribution for parameter a + "D": cp.Triangle(0.75, 0.8, 0.85) # Triangular distribution for parameter D } +# Set the sampling method to use Polynomial Chaos Expansion (PCE) for sensitivity analysis campaign.set_sampler(uq.sampling.PCESampler(vary=vary, polynomial_order=1)) -with QCGPJPool(template_params={'venv': '/home/bartek/.virtualenv/qcgpj7'}) as qcgpj: -#with QCGPJPool() as qcgpj: +# Run the campaign with a parallel pool using QCGPJ (a parallel job pool) +with QCGPJPool() as qcgpj: + # Execute the campaign with the defined pool and then collate the results campaign.execute(pool=qcgpj).collate() +# Get the collation results from the campaign campaign.get_collation_result() +# Dump the campaign database as JSON for debugging purposes campaign.campaign_db.dump() +# Perform the analysis on the output quantities (in this case, 'g1') results = campaign.analyse(qoi_cols=['g1']) -results.plot_sobols_treemap('g1', figsize=(10, 10)) -plt.axis('off') -results.sobols_first('g1') -results.supported_stats() -results._get_sobols_first('g1', 'F') -results.sobols_total('g1', 'F') - -print("success") + +# Plot the Sobol indices as a treemap and save it to a file +results.plot_sobols_treemap('g1', figsize=(10, 10)) # Create the Sobol indices treemap plot +plt.axis('off') # Turn off the axis for a cleaner plot +plt.savefig('sobols_treemap.png', bbox_inches='tight') # Save the plot to a file +plt.show() # Display the plot + +# Perform additional analysis on the Sobol indices and print the results +results.sobols_first('g1') # First-order Sobol indices +results.supported_stats() # Get the supported statistical measures +results._get_sobols_first('g1', 'F') # First-order Sobol index for parameter 'F' +results.sobols_total('g1', 'F') # Total Sobol index for parameter 'F' + +print("success") # Print success message after all tasks are complete + From 04ce019d0b0e6c1be2af09eb411a0c085a835ce1 Mon Sep 17 00:00:00 2001 From: Derek Groen Date: Wed, 4 Dec 2024 13:11:12 +0000 Subject: [PATCH 41/42] Added setuptools_scm dependency which is apparently required for test_mcmc.py. --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 75a3aa1cb..3f7facd38 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,6 +34,7 @@ dependencies = [ "h5py", "tomli", "fipy", + "setuptools_scm", ] [project.optional-dependencies] From 1944d15165100205ba3fcb62351e4769abf3cbf2 Mon Sep 17 00:00:00 2001 From: Jon McCullough Date: Wed, 4 Dec 2024 13:34:49 +0000 Subject: [PATCH 42/42] Edits to mc_sampler to reflect SC/PCE capability for DiscreteUniform distribution --- easyvvuq/sampling/mc_sampler.py | 9 ++++++++- tests/test_mix_continuous_discrete.py | 12 ++++++++++++ 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/easyvvuq/sampling/mc_sampler.py b/easyvvuq/sampling/mc_sampler.py index 5c6d311a2..77192408d 100644 --- a/easyvvuq/sampling/mc_sampler.py +++ b/easyvvuq/sampling/mc_sampler.py @@ -52,6 +52,8 @@ def __init__(self, vary, n_mc_samples, **kwargs): super().__init__(vary=vary, count=0, max_num=n_mc_samples, **kwargs) # the number of uncertain inputs self.n_params = len(vary) + # List of the probability distributions of uncertain parameters + self.params_distribution = list(vary.values()) # the number of MC samples, for each of the n_params + 2 input matrices self.n_mc_samples = n_mc_samples # joint distribution @@ -67,7 +69,12 @@ def __next__(self): run_dict = {} for idx, param_name in enumerate(self.vary.get_keys()): - run_dict[param_name] = self.xi_mc[self.count][idx] + current_param = self.xi_mc[self.count][idx] + if isinstance(self.params_distribution[idx], cp.DiscreteUniform): + current_param = int(current_param) + run_dict[param_name] = current_param + + self.count += 1 return run_dict diff --git a/tests/test_mix_continuous_discrete.py b/tests/test_mix_continuous_discrete.py index ddf086091..b8e706bf4 100644 --- a/tests/test_mix_continuous_discrete.py +++ b/tests/test_mix_continuous_discrete.py @@ -72,3 +72,15 @@ def test_pce(get_campaign): df = campaign.get_collation_result() assert df.values[0][-1] == 'float' assert df.values[0][-2] == 'int' + +def test_mc(get_campaign): + """ + Perform the test for the MC sampler + """ + campaign, vary = get_campaign + sampler = uq.sampling.MCSampler(vary=vary, n_mc_samples=1) + campaign.set_sampler(sampler) + campaign.execute().collate() + df = campaign.get_collation_result() + assert df.values[0][-1] == 'float' + assert df.values[0][-2] == 'int'