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JCGoran · Mar 13, 2024 · c7f38da · c7f38da
1 parent a31f17d
commit c7f38da
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Showing 8 changed files with 81 additions and 122 deletions.
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
@@ -22,28 +22,24 @@ jobs:
   deploy-book:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     # Install dependencies
     - name: Set up Python 3.9
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
-    - name: Install Poetry
-      uses: snok/install-poetry@v1
-
     - name: Install dependencies
       run: |
-        python3 -m pip install pdoc matplotlib numpy scipy wheel setuptools poetry pytest
-        python3 -m pip install .
+        python3 -m pip install .[docs,test]
 
     # Build the site
     - name: Build the site
       run: |
-        bash generate_docs.sh -t
+        bash scripts/generate_docs.sh -t
 
     # If we've pushed to master, push the book's HTML to github-pages
     - if: ${{ github.ref == 'refs/heads/master' }}

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -21,69 +21,47 @@ jobs:
       #----------------------------------------------
       #       check-out repo and set-up python
       #----------------------------------------------
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      #----------------------------------------------
-      #        poetry setup
-      #----------------------------------------------
-      - uses: snok/install-poetry@v1
-        with:
-          version: 1.4.2
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-      - name: cache deps
-        id: cache-deps
-        uses: actions/cache@v2
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          path: .venv
-          key: pydeps-${{ hashFiles('**/poetry.lock') }}
-      - run: poetry install --extras interfaces --no-interaction --no-root
-        if: steps.cache-deps.outputs.cache-hit != 'true'
-      - run: poetry install --no-interaction
-      #----------------------------------------------
-      #          install and run linters
-      #----------------------------------------------
-      - run: sh check_syntax.sh
+          python-version: '3.9'
+
+      - run: |
+          python -m pip install .[docs,test]
+
+      - run: bash scripts/check_syntax.sh
+
   test:
     name: Tests of general module
     needs: linting
     strategy:
       fail-fast: true
       matrix:
         os: [ "ubuntu-latest" ]
-        python-version: [ "3.7", "3.8", "3.9" ]
+        python-version: [ "3.7", "3.9", "3.12" ]
 
     runs-on: ${{ matrix.os }}
     steps:
       #----------------------------------------------
       #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
+
       - name: Set up python ${{ matrix.python-version }}
         id: setup-python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      #----------------------------------------------
-      #        poetry setup
-      #----------------------------------------------
-      - uses: snok/install-poetry@v1
-        with:
-          version: 1.4.2
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-      - name: cache deps
-        id: cache-deps
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: pydeps-${{ hashFiles('**/poetry.lock') }}
-      - run: poetry install --no-interaction --no-root
-        if: steps.cache-deps.outputs.cache-hit != 'true'
-      - run: poetry install --no-interaction
+
+      - run: |
+          python -m pip install .[test]
+
       - name: Run tests
-        run: sh check_coverage.sh
+        run: bash scripts/check_coverage.sh
+
       - name: Upload coverage
         if: ${{ matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest' }}
         uses: codecov/codecov-action@v1
@@ -103,31 +81,20 @@ jobs:
       #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v2
-      #----------------------------------------------
-      #        poetry setup
-      #----------------------------------------------
-      - uses: snok/install-poetry@v1
-        with:
-          version: 1.4.2
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-      - name: cache deps
-        id: cache-deps
-        uses: actions/cache@v2
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          path: .venv
-          key: pydeps-${{ hashFiles('**/poetry.lock') }}
-      - run: poetry install --no-interaction --no-root
-        if: steps.cache-deps.outputs.cache-hit != 'true'
-      - run: poetry install --no-interaction
-      - name: Install CLASS
+          python-version: '3.9'
+
+      - name: Install project and CLASS
         run: |
-          poetry install --no-interaction
-          poetry run pip install Cython
-          git clone --depth 1 --branch feature/conda https://github.com/JCGoran/class_public && cd class_public && poetry run make classy && cd -
+          python -m pip install .[test]
+          python -m pip install Cython
+          git clone --depth 1 --branch feature/conda https://github.com/JCGoran/class_public && cd class_public && make classy && cd -
       - name: Run CLASS tests
-        run: poetry run pytest -v tests/test_classy_interfaces.py
+        run: python -m pytest -v tests/test_classy_interfaces.py
 
   coffe:
     name: Tests for COFFE interfaces
@@ -136,32 +103,21 @@ jobs:
     strategy:
       fail-fast: true
     steps:
-      #----------------------------------------------
-      #       check-out repo and set-up python
-      #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v2
-      #----------------------------------------------
-      #        poetry setup
-      #----------------------------------------------
-      - uses: snok/install-poetry@v1
-        with:
-          version: 1.4.2
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-      - name: cache deps
-        id: cache-deps
-        uses: actions/cache@v2
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          path: .venv
-          key: pydeps-${{ hashFiles('**/poetry.lock') }}
-      - run: poetry install --no-interaction --no-root
-        if: steps.cache-deps.outputs.cache-hit != 'true'
-      - run: poetry install --no-interaction
-      - name: Install COFFE
-        run: poetry install --extras coffe --no-interaction
+          python-version: '3.9'
+
+      - name: Install project and COFFE
+      - run: |
+          python -m pip install .[test]
+          python -m pip install coffe
+
       - name: Run COFFE tests
-        run: poetry run pytest -v tests/test_coffe_interfaces.py
+        run: python -m pytest -v tests/test_coffe_interfaces.py
 
   camb:
     name: Tests for CAMB interfaces
@@ -170,29 +126,18 @@ jobs:
     strategy:
       fail-fast: true
     steps:
-      #----------------------------------------------
-      #       check-out repo and set-up python
-      #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v2
-      #----------------------------------------------
-      #        poetry setup
-      #----------------------------------------------
-      - uses: snok/install-poetry@v1
-        with:
-          version: 1.4.2
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-      - name: cache deps
-        id: cache-deps
-        uses: actions/cache@v2
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          path: .venv
-          key: pydeps-${{ hashFiles('**/poetry.lock') }}
-      - run: poetry install --no-interaction --no-root
-        if: steps.cache-deps.outputs.cache-hit != 'true'
-      - run: poetry install --no-interaction
+          python-version: '3.9'
+
       - name: Install CAMB
-        run: poetry install --extras camb --no-interaction
+        run: |
+          python -m pip install .[test]
+          python -m pip install camb
+
       - name: Run CAMB tests
-        run: poetry run pytest -v tests/test_camb_interfaces.py
+        run: python -m pytest -v tests/test_camb_interfaces.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -31,18 +31,19 @@ docs = [
     "pdoc",
     "pydocstyle",
 ]
+dev = [
+    "black",
+    "pylint",
+    "mypy",
+]
 
 [project.urls]
 documentation = "https://jcgoran.github.io/fitk/"
 repository = "https://github.com/JCGoran/fitk/"
 
 [tool.poetry.dev-dependencies]
-black = "*"
-pylint = "*"
-mypy = "*"
 jupyterlab = "*"
 vermin = "*"
-coverage = "*"
 python-lsp-server = "*"
 pydocstyle = "*"
 

diff --git a/scripts/check_coverage.sh b/scripts/check_coverage.sh
@@ -5,7 +5,9 @@
 set -eux
 
 check_coverage(){
+    this_dir="$(cd "$(dirname "$0")"; pwd -P)"
     excluded='not __init__.py and not interfaces'
+    cd "${this_dir}/.."
     if [ "${1:-}" = '-i' ] || [ "${1:-}" = '--images' ]
     then
         python -m pytest --mpl --doctest-modules --mpl-generate-summary=html -k "${excluded}" --cov=python/fitk/ --cov=tests/ --cov-report=xml tests/ python/fitk/
@@ -14,6 +16,7 @@ check_coverage(){
     fi
     python -m coverage html
     python -m coverage report
+    cd - > /dev/null
 }
 
 check_coverage "${1:-}"

diff --git a/scripts/check_syntax.sh b/scripts/check_syntax.sh
@@ -4,11 +4,14 @@ set -eux
 
 validate(){
     modules='python/fitk/ tests/'
+    this_dir="$(cd "$(dirname "$0")"; pwd -P)"
+    cd "${this_dir}/.."
     python -m black --check ${modules}
     # the E0611 is because Pylint detects some native modules (like
     # `collections.abc.Collection`) as missing on some machines for one reason
     # or another
     python -m pylint --disable=W,R,C,E0611 ${modules}
+    cd - > /dev/null
 }
 
 validate

diff --git a/scripts/fix_formatting.sh b/scripts/fix_formatting.sh
@@ -4,7 +4,10 @@ set -eux
 
 fix(){
     modules='python/fitk/ tests/'
+    this_dir="$(cd "$(dirname "$0")"; pwd -P)"
+    cd "${this_dir}/.."
     python -m black ${modules}
+    cd - > /dev/null
 }
 
 fix

diff --git a/scripts/generate_docs.sh b/scripts/generate_docs.sh
@@ -4,6 +4,8 @@
 
 set -eu
 
+this_dir="$(cd "$(dirname "$0")"; pwd -P)"
+cd "${this_dir}/.."
 # the name of the package
 PACKAGE='fitk'
 export PACKAGE
@@ -61,4 +63,6 @@ else
     parse_docs ./docs
 fi
 
+cd - > /dev/null
+
 set +eu
diff --git a/scripts/generate_test_images.sh b/scripts/generate_test_images.sh
@@ -4,9 +4,13 @@
 
 set -eux
 
+this_dir="$(cd "$(dirname "$0")"; pwd -P)"
+cd "${this_dir}/.."
 image_directory='tests/data_input/'
 modules="${1:-tests/test_graphics.py}"
 
 python -m pytest --mpl-generate-path="${image_directory}" "${modules}"
 
+cd - > /dev/null
+
 set +eux