Miscellaneous

.env

@@ -0,0 +1,2 @@
+# Greatly improves performance and reproducibility
+OMP_NUM_THREADS=1

.gcloudignore

@@ -0,0 +1,8 @@
+#!include:.gitignore
+notebooks
+data
+reconstruction/sim_data
+reconstruction/ecoli/scripts
+.git
+.github
+doc

.github/workflows/docs_deploy.yml

@@ -9,23 +9,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Setup Python
-        uses: actions/setup-python@v2
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
         with:
-          python-version: "3.11"
-      - name: Install dependencies
-        run: |
-          sudo apt-get install pandoc
-          python -m pip install --upgrade pip wheel
-          pip install numpy==1.26.4
-          pip install -r doc/requirements.txt
-      - name: Compile Cython components
-        run: |
-          make compile
+          enable-cache: true
+          version: "0.5.7"
+      - name: Install Pandoc
+        run: sudo apt-get install pandoc
+      - name: Install model
+        run: USE_CYTHON=1 uv sync --frozen --extra docs
       - name: Build documentation
         run: |
           cd doc
-          make html
+          uv run make html
       - name: Deploy documentation to GitHub pages
         run: |
           cd doc/_build/html

.github/workflows/docs_test.yml

@@ -11,20 +11,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Setup Python
-        uses: actions/setup-python@v2
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
         with:
-          python-version: "3.11"
-      - name: Install dependencies
-        run: |
-          sudo apt-get install pandoc
-          python -m pip install --upgrade pip wheel
-          pip install numpy==1.26.4
-          pip install -r doc/requirements.txt
-      - name: Compile Cython components
-        run: |
-          make compile
+          enable-cache: true
+          version: "0.5.7"
+      - name: Install Pandoc
+        run: sudo apt-get install pandoc
+      - name: Install model
+        run: USE_CYTHON=1 uv sync --frozen --extra docs
       - name: Build documentation
         run: |
           cd doc
-          make html
+          uv run make html

.github/workflows/pr_tests.yml

@@ -2,11 +2,6 @@
 
 name: Workflow
 
-# Improves reproducibility and speed
-env:
-  OPENBLAS_NUM_THREADS: 1
-  OMP_NUM_THREADS: 1
-
 on:
   push:
     branches: [master]
@@ -16,72 +11,50 @@ on:
 jobs:
   Reproducibility:
     runs-on: macos-latest
-    strategy:
-      matrix:
-        python-version: ["3.11"]
     steps:
     - uses: actions/checkout@v2
-    - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip wheel
-        pip install numpy==1.26.4
-        pip install -r requirements.txt
-    - name: Compile Cython components
-      run: |
-        make clean compile
-    - name: Set PYTHONPATH
-      run: |
-        echo "PYTHONPATH=." >> $GITHUB_ENV
+        enable-cache: true
+        version: "0.5.7"
+    - name: Install model
+      run: USE_CYTHON=1 uv sync --frozen
     - name: Test ParCa reproducibility
       run: |
-        python runscripts/parca.py --config ecoli/composites/ecoli_configs/run_parca.json \
+        uv run --env-file .env runscripts/parca.py --config ecoli/composites/ecoli_configs/run_parca.json \
             -c 3 -o out/parca_1
-        python runscripts/parca.py --config ecoli/composites/ecoli_configs/run_parca.json \
+        uv run --env-file .env runscripts/parca.py --config ecoli/composites/ecoli_configs/run_parca.json \
             -c 3 -o out/parca_2
-        python runscripts/debug/compare_pickles.py out/parca_1/kb out/parca_2/kb
+        uv run --env-file .env runscripts/debug/compare_pickles.py out/parca_1/kb out/parca_2/kb
     - name: Test simulation reproducibility
       run: |
-        python ecoli/experiments/ecoli_master_sim.py \
+        uv run --env-file .env ecoli/experiments/ecoli_master_sim.py \
             --generations 1 --emitter parquet --emitter_arg out_dir='out' \
             --experiment_id "parca_1" --daughter_outdir "out/parca_1" \
             --sim_data_path "out/parca_1/kb/simData.cPickle" --fail_at_total_time &
-        python ecoli/experiments/ecoli_master_sim.py \
+        uv run --env-file .env ecoli/experiments/ecoli_master_sim.py \
             --generations 1 --emitter parquet --emitter_arg out_dir='out' \
             --experiment_id "parca_2" --daughter_outdir "out/parca_2" \
             --sim_data_path "out/parca_2/kb/simData.cPickle" --fail_at_total_time
-        python runscripts/debug/diff_simouts.py -o "out" "parca_1*" "parca_2*"
+        uv run --env-file .env runscripts/debug/diff_simouts.py -o "out" "parca_1*" "parca_2*"
   Two-gens:
     runs-on: macos-latest
-    strategy:
-      matrix:
-        python-version: ["3.11"]
     steps:
     - uses: actions/checkout@v2
-    - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip wheel
-        pip install numpy==1.26.4 mypy
-        pip install -r requirements.txt
+        enable-cache: true
+        version: "0.5.7"
+    - name: Install model
+      run: USE_CYTHON=1 uv sync --frozen
     - name: Install nextflow edge
       run: |
         curl -s https://get.nextflow.io | bash
         chmod +x nextflow
         echo "PATH=.:$PATH" >> $GITHUB_ENV
         NXF_EDGE=1 ./nextflow self-update
-    - name: Compile Cython components
-      run: |
-        make clean compile
-    - name: Set PYTHONPATH
-      run: |
-        echo "PYTHONPATH=." >> $GITHUB_ENV
     - name: Two generations
       run: |
-        python runscripts/workflow.py --config ecoli/composites/ecoli_configs/two_generations.json
+        uv run --env-file .env runscripts/workflow.py --config ecoli/composites/ecoli_configs/two_generations.json

.github/workflows/pytest.yml

@@ -2,11 +2,6 @@
 
 name: QA
 
-# Improves reproducibility and speed
-env:
-  OPENBLAS_NUM_THREADS: 1
-  OMP_NUM_THREADS: 1
-
 on:
   push:
     branches: [master]
@@ -16,26 +11,18 @@ on:
 jobs:
   Pytest:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.11"]
     steps:
     - uses: actions/checkout@v2
-    - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip wheel
-        pip install numpy==1.26.4
-        pip install -r requirements.txt
-    - name: Compile Cython components
-      run: |
-        make clean compile
+        enable-cache: true
+        version: "0.5.7"
+    - name: Install model
+      run: USE_CYTHON=1 uv sync --frozen --extra dev
     - name: Test with pytest
       run: |
-        python -m pytest --cov-report xml:cov.xml --cov=ecoli --cov=reconstruction --cov=wholecell --cov=runscripts --durations=0
+        uv run --env-file .env pytest --cov-report xml:cov.xml --cov=ecoli --cov=reconstruction --cov=wholecell --cov=runscripts --durations=0
     - name: Code Coverage Report
       uses: irongut/[email protected]
       with:
@@ -51,45 +38,29 @@ jobs:
         path: code-coverage-results.md
   Mypy:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.11"]
     steps:
     - uses: actions/checkout@v2
-    - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip wheel
-        pip install numpy==1.26.4 mypy
-        pip install -r requirements.txt
-    - name: Compile Cython components
-      run: |
-        make clean compile
+        enable-cache: true
+        version: "0.5.7"
+    - name: Install model
+      run: USE_CYTHON=1 uv sync --frozen --extra dev
     - name: Mypy
       run: |
-        mypy
+        uv run --env-file .env mypy
   Lint:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.11"]
     steps:
     - uses: actions/checkout@v2
-    - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip wheel
-        pip install numpy==1.26.4 ruff
-        pip install -r requirements.txt
-    - name: Compile Cython components
-      run: |
-        make clean compile
+        enable-cache: true
+        version: "0.5.7"
+    - name: Install model
+      run: USE_CYTHON=1 uv sync --frozen --extra dev
     - name: Ruff
       run: |
-        ruff check doc ecoli migration wholecell runscripts validation reconstruction
+        uv run --env-file .env ruff check doc ecoli migration wholecell runscripts validation reconstruction

.gitignore

@@ -3,7 +3,7 @@
 /build
 /dist
 /doc/_build
-/vivarium_ecoli.egg-info
+/vEcoli.egg-info
 /Build_sequences.egg-info
 /Fast_polymerize_sums.egg-info
 /Monte_carlo_complexation.egg-info
@@ -37,17 +37,12 @@ __pycache__
 ._*
 .python-version
 .pytest_cache
-
-# Pipenv files #
-################
-Pipfile
-Pipfile.lock
-pyproject.toml
+.mypy_cache/
+.ruff_cache/
 
 # VS Code files #
 #################
 /.vscode
-/.env
 
 # Generated Files #
 ###################
@@ -61,8 +56,9 @@ cache/
 ##################
 .nextflow*
 nextflow_temp
+trace-*
+
+# Virtual environment #
+#######################
+.venv/
 
-# Other files #
-##################
-/notebooks/ck/
-/notebooks/ck_example/