add modifications for 2024 session (#5)

* add modifications for 2024 session

* add linters to optional dependencies

* run isort

.github/workflows/cd.yml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
@@ -31,7 +31,7 @@ jobs:
           sphinx-build docs/source docs/build
 
       - name: Deploy API documentation
-        uses: peaceiris/actions-gh-pages@v3.5.9
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: docs/build

.github/workflows/ci.yml

@@ -18,18 +18,23 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        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: Check Python version
         run: python --version
 
       - name: Install dependencies
-        run: python -m pip install ".[test]"
+        run: python -m pip install ".[lint,test]"
 
-      - name: Run tests
-        run: python -m pytest
+      - name: Run unit tests
+        run: python -m pytest
+
+      - name: Run linting tests
+        run: |
+          black --check .
+          isort --check .

.github/workflows/deploy-image.yml

@@ -17,7 +17,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Log in to the Container registry
         uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9

.github/workflows/verify.yml

@@ -0,0 +1,32 @@
+name: Verification
+
+on: workflow_dispatch
+
+jobs:
+  test-full:
+    name: Run Verification Tests
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.11"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Check Python version
+        run: python --version
+
+      - name: Install dependencies
+        run: python -m pip install ".[test,verify]"
+
+      - name: Run unit tests
+        run: python -m pytest scripts/astropy_verification.py

.gitlab-ci.yml

@@ -2,12 +2,14 @@ image: python:latest
 
 before_script:
   - python --version 
-  - python -m pip install ".[docs,test]"
+  - python -m pip install ".[dev]"
 
 test:
   coverage: '/(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'
   script:
     - python -m pytest
+    - black --check .
+    - isort --check .
   only:
     refs:
       - merge_requests
@@ -16,7 +18,6 @@ test:
 Verification:
   script:
     - export TF_CPP_MIN_LOG_LEVEL=1
-    - python -m pip install astropy
     - python -m pytest scripts/astropy_verification.py
   when: manual
   only:

Dockerfile

@@ -5,8 +5,11 @@ WORKDIR /home
 ENV SHELL /bin/bash
 
 RUN apt-get update
-RUN apt-get install build-essential -y
+RUN apt-get install -y build-essential && \
+    apt-get install -y nano
 
 COPY * .
 
-RUN conda env create -f environment.yml
+RUN conda env create -f environment.yml
+
+RUN echo "conda activate mycosmo" >> ~/.bashrc

README.md

@@ -4,6 +4,8 @@
 
 This repository was made for a course on scientific software development at the [2023 edition of the Euclid Summer School](https://ecole-euclid.cnrs.fr/2023-accueil/).
 
+> The content was updated for the [2024 edition of the Rodolphe Clédassou Summer School](https://ecole-euclid.cnrs.fr/2024-accueil/)
+
 The slides accompanying this repository can be found [here](https://sfarrens.github.io/presentations/#/).
 
 Example API documentation can be found [here](https://sfarrens.github.io/ecole-euclid-2023/).
@@ -13,11 +15,12 @@ Example API documentation can be found [here](https://sfarrens.github.io/ecole-e
 To follow this course you will need to have Python (ideally v3.11) installed with the following dependencies:
 
 - numpy
+- astropy
 - black
+- isort
 - myst-parser
 - numpydoc
 - pytest
-- pytest-black
 - pytest-pydocstyle
 - pytest-emoji
 - pytest-cov
@@ -53,12 +56,12 @@ Finally, you can avoid installing any of the packages by simply pulling the prov
 
 ```bash
 docker pull ghcr.io/sfarrens/ecole-euclid-2023:main
-docker tag ghcr.io/sfarrens/ecole-euclid-2023:main ecole-euclid-2023
+docker tag ghcr.io/sfarrens/ecole-euclid-2023:main ecole-rc-2024
 ```
 
 Then you can launch an interactive container as follows:
 
 ```bash
-docker run -it ecole-euclid-2023
+docker run -it ecole-rc-2024
 conda activate mycosmo
 ```

docs/source/conf.py

@@ -3,9 +3,8 @@
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-import sys
 import os
-
+import sys
 
 sys.path.insert(0, os.path.abspath("../.."))
 

environment.yml

@@ -4,11 +4,13 @@ channels:
 dependencies:
   - python=3.11
   - numpy>=1.25
+  - astropy
   - black
+  - build
+  - isort
   - myst-parser
   - numpydoc
   - pytest
-  - pytest-black
   - pytest-emoji
   - pytest-cov
   - sphinx

mycosmo/cosmology.py

@@ -6,7 +6,7 @@
 
 import numpy as np
 
-from .constants import Mpc, G
+from .constants import G, Mpc
 
 
 def hubble(redshift, cosmo_dict):

mycosmo/tests/test_cosmology.py

@@ -1,7 +1,7 @@
 import numpy as np
 import numpy.testing as npt
 
-from mycosmo.cosmology import hubble, critical_density
+from mycosmo.cosmology import critical_density, hubble
 
 
 class TestCosmology:

pyproject.toml

@@ -10,25 +10,22 @@ version = "0.0.1"
 
 [project.optional-dependencies]
 docs = ["myst-parser", "numpydoc", "sphinx", "sphinx-book-theme"]
-lint = ["black"]
+lint = ["black", "isort"]
 release = ["build", "twine"]
 test = [
     "pytest",
-    "pytest-black",
     "pytest-cov",
     "pytest-emoji",
     "pytest-pydocstyle",
 ]
+verify = ["astropy"]
 
 # Install for development
 dev = ["mycosmo[docs,lint,release,test]"]
 
-[tool.black]
-line-length = 88
-
 [tool.pydocstyle]
 convention = "numpy"
 
 [tool.pytest.ini_options]
-addopts = ["--verbose", "--black", "--emoji", "--pydocstyle", "--cov=mycosmo"]
+addopts = ["--verbose", "--emoji", "--pydocstyle", "--cov=mycosmo"]
 testpaths = ["mycosmo"]

scripts/astropy_verification.py

@@ -7,7 +7,7 @@
 import numpy as np
 from astropy.cosmology import WMAP9 as cosmo
 
-from mycosmo.cosmology import hubble, critical_density
+from mycosmo.cosmology import critical_density, hubble
 
 
 class TestAstropy: