From 398b9bf572ee2b1360445494014428ea3e4c198a Mon Sep 17 00:00:00 2001 From: JoelLucaAdams Date: Tue, 29 Oct 2024 15:28:21 +0000 Subject: [PATCH 1/5] Rework README --- README.md | 127 ++++++++++++++++++++++++++++-------------------------- 1 file changed, 66 insertions(+), 61 deletions(-) diff --git a/README.md b/README.md index 939470e..28491c6 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,72 @@ # epydeck -An EPOCH input file ("deck") reader/writer. +An EPOCH plasma PIC code input file (deck) reader/writer. -Plain numbers and bools are converted directly, everything else is -represented as a string. Note that floating point numbers may have -their exact form changed. +> [!IMPORTANT] +> Plain numbers and bools are converted directly, everything else is +> represented as a string. Note that floating point numbers may have +> their exact form changed. + +## Installation + +Install from PyPI with: + +```bash +pip install epydeck +``` + +or from local checkout: + +```bash +git clone https://github.com/PlasmaFAIR/epydeck.git +cd epydeck +pip install . +``` + +We recommend switching to [uv](https://docs.astral.sh/uv/) to manage packages. + +## Usage + +The interface follows the standard Python +[`json`](https://docs.python.org/3/library/json.html) module: + +- `epydeck.load` to read from a `file` object +- `epydeck.loads` to read from an existing string +- `epydeck.dump` to write to a `file` object +- `epydeck.dumps` to write to a string + +```python +import epydeck + +# Read from a file with `epydeck.load` +with open(filename) as f: + deck = epydeck.load(f) + +print(deck.keys()) +# dict_keys(['control', 'boundaries', 'constant', 'species', 'laser', 'output_global', 'output', 'dist_fn']) + +# Modify the deck as a usual python dict: +deck["species"]["proton"]["charge"] = 2.0 + +# Write to file +with open(filename, "w") as f: + epydeck.dump(deck, f) + +print(epydeck.dumps(deck)) +# ... +# begin:species +# name = proton +# charge = 2.0 +# mass = 1836.2 +# fraction = 0.5 +# number_density = if((r gt ri) and (r lt ro), den_cone, 0.0) +# number_density = if((x gt xi) and (x lt xo) and (r lt ri), den_cone, number_density(proton)) +# number_density = if(x gt xo, 0.0, number_density(proton)) +# end:species +# ... +``` + +## Further Examples Reads from file into a standard Python `dict`. Repeated blocks, such as `species`, have an extra level of nesting using the block `name`. @@ -81,60 +143,3 @@ is represented by the following `dict`: } } ``` - -## Installation - -Currently just on Github, so either install from a local clone: - -```bash -$ git clone git@github.com:PlasmaFAIR/epydeck.git -$ cd epydeck -$ pip install . -``` - -or directly from Github: - -```bash -$ pip install git@github.com:PlasmaFAIR/epydeck.git -``` - -## Example - -The interface follows the standard Python -[`json`](https://docs.python.org/3/library/json.html) module: - -- `epydeck.load` to read from a `file` object -- `epydeck.loads` to read from an existing string -- `epydeck.dump` to write to a `file` object -- `epydeck.dumps` to write to a string - -```python -import epydeck - -# Read from a file with `epydeck.load` -with open(filename) as f: - deck = epydeck.load(f) - -print(deck.keys()) -# dict_keys(['control', 'boundaries', 'constant', 'species', 'laser', 'output_global', 'output', 'dist_fn']) - -# Modify the deck as a usual python dict: -deck["species"]["proton"]["charge"] = 2.0 - -# Write to file -with open(filename, "w") as f: - epydeck.dump(deck, f) - -print(epydeck.dumps(deck)) -# ... -# begin:species -# name = proton -# charge = 2.0 -# mass = 1836.2 -# fraction = 0.5 -# number_density = if((r gt ri) and (r lt ro), den_cone, 0.0) -# number_density = if((x gt xi) and (x lt xo) and (r lt ri), den_cone, number_density(proton)) -# number_density = if(x gt xo, 0.0, number_density(proton)) -# end:species -# ... -``` From 9411b26162d780819b9a32f703127e85e03f7922 Mon Sep 17 00:00:00 2001 From: JoelLucaAdams Date: Tue, 29 Oct 2024 15:28:44 +0000 Subject: [PATCH 2/5] Fix missing parameters in pyproject.toml --- pyproject.toml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 2a41a11..f175e29 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,25 +8,25 @@ build-backend = "setuptools.build_meta" [project] name = "epydeck" +readme = "README.md" authors = [ - {name = "Peter Hill", email = "peter.hill@york.ac.uk"}, - {name = "Joel Adams", email = "joel.adams@york.ac.uk"} + { name = "Peter Hill", email = "peter.hill@york.ac.uk" }, + { name = "Joel Adams", email = "joel.adams@york.ac.uk" }, ] -license = {text = "BSD"} +license = { file = "LICENCE.md" } requires-python = ">=3.9" dynamic = ["version"] +description = "An EPOCH plasma PIC code input file (deck) reader/writer." [project.optional-dependencies] docs = [ - "sphinx >= 5.3", - "sphinx_autodoc_typehints >= 1.19", - "sphinx-book-theme >= 0.4.0rc1", - "sphinx-argparse-cli >= 1.10.0", - "sphinx-inline-tabs", -] -tests = [ - "pytest >= 3.3.0", + "sphinx >= 5.3", + "sphinx_autodoc_typehints >= 1.19", + "sphinx-book-theme >= 0.4.0rc1", + "sphinx-argparse-cli >= 1.10.0", + "sphinx-inline-tabs", ] +tests = ["pytest >= 3.3.0"] [tool.setuptools_scm] write_to = "src/epydeck/_version.py" From fb1b1fee170266d50bdb85f744b5f38c0c4ae0fd Mon Sep 17 00:00:00 2001 From: JoelLucaAdams Date: Tue, 29 Oct 2024 15:28:54 +0000 Subject: [PATCH 3/5] Add publish workflow --- .github/workflows/build_publish.yml | 49 +++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 .github/workflows/build_publish.yml diff --git a/.github/workflows/build_publish.yml b/.github/workflows/build_publish.yml new file mode 100644 index 0000000..eeb1ee0 --- /dev/null +++ b/.github/workflows/build_publish.yml @@ -0,0 +1,49 @@ +name: Build/publish Python Package + +on: push + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.x' + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install build twine + - name: Build package + run: | + python -m build --sdist --wheel + - name: Check package + run: | + python -m twine check dist/* + - name: Store the distribution packages + uses: actions/upload-artifact@v4 + with: + name: python-package-distributions + path: dist/ + + publish-to-pypi: + if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes + needs: + - build + runs-on: ubuntu-latest + environment: + name: release + url: https://pypi.org/p/epydeck + permissions: + id-token: write # IMPORTANT: mandatory for trusted publishing + steps: + - name: Download distribution packages + uses: 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family-names: Adams + given-names: Joel L. + orcid: 'https://orcid.org/0009-0005-4889-5231' + affiliation: University of York +repository-code: 'https://github.com/PlasmaFAIR/epydeck' +date-released: '2024-04-22'