Merge pull request #81 from linea-it/doc_error

Bug fix in validation of documentation construction.

.devcontainer/Dockerfile

@@ -3,8 +3,8 @@ FROM mcr.microsoft.com/devcontainers/python:0-3.10
 ENV PYTHONUNBUFFERED 1
 
 # [Optional] If your requirements rarely change, uncomment this section to add them to the image.
-COPY docs/requirements.txt /tmp/pip-tmp/
-RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements.txt \
+COPY requirements-dev.txt /tmp/pip-tmp/
+RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements-dev.txt \
    && rm -rf /tmp/pip-tmp
 
 RUN apt-get update && apt-get -y install pandoc

.github/workflows/build-documentation.yml

@@ -24,13 +24,13 @@ jobs:
         pip install .
         pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
     - name: Install notebook requirements
       run: |
         sudo apt-get install pandoc
     - name: Build docs
       run: |
-        sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html
+        sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html -D exclude_patterns="notebooks/*"
     - name: Run ghp-import
       run: | 
         ghp-import -n -p -f -x docs/ docs/build/html

.github/workflows/linting.yml

@@ -30,6 +30,7 @@ jobs:
         pip install .
         pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
     - name: Analyze code with linter
 
       run: |

.github/workflows/smoke-test.yml

@@ -28,6 +28,7 @@ jobs:
         pip install .
         pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
     - name: Run unit tests with pytest
       run: |
         python -m pytest tests

.github/workflows/testing-and-coverage.yml

@@ -30,6 +30,7 @@ jobs:
         pip install .
         pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
     - name: Run unit tests with pytest
       run: |
         python -m pytest tests --cov=pzserver --cov-report=xml

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     # This hook should always pass. It will print a message if the local version 
     # is out of date.
   - repo: https://github.com/lincc-frameworks/pre-commit-hooks
-    rev: v0.1
+    rev: v0.1.2
     hooks:
       - id: check-lincc-frameworks-template-version
         name: Check template version
@@ -40,7 +40,7 @@ repos:
 
     # prevents committing directly branches named 'main' and 'master'.
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: no-commit-to-branch
         name: Prevent main branch commits
@@ -52,15 +52,15 @@ repos:
 
     # verify that pyproject.toml is well formed
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.12.1
+    rev: v0.16
     hooks:
       - id: validate-pyproject
         name: Validate pyproject.toml
         description: Verify that pyproject.toml adheres to the established schema.
 
     # Automatically sort the imports used in .py files
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python files in src/ and tests/)

docs/notebooks/intro_notebook.ipynb

@@ -11,7 +11,7 @@
     "\n",
     "Contact author: [Julia Gschwend](mailto:[email protected])\n",
     "\n",
-    "Last verified run: 2024-Jan-23<br>"
+    "Last verified run: 2024-May-06<br>"
    ]
   },
   {
@@ -927,9 +927,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "pz-lib",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "pz-lib"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "pzserver"
 license = {file = "LICENSE"}
-dynamic = ["version"]
+dynamic = ["version", "dependencies", "optional-dependencies"]
 readme = "README.md"
 authors = [
     { name = "LIneA", email = "[email protected]" }
@@ -20,40 +20,6 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
 ]
-dependencies = [
-    "deprecated",
-    "numpy>=1.23",
-    "pandas>=1.2.0",
-    "requests>=2.23.0",
-    "astropy>=5.0.0",
-    "matplotlib>=3.6.0",
-    "tables_io>=0.7.9",
-    "Jinja2>=3.1.2",
-    "ipython>=8.5.0",
-    "h5py>=3.8.0",
-    "pyarrow>=15.0.2",
-]
-
-# On a mac, install optional dependencies with `pip install '.[dev]'` (include the single quotes)
-[project.optional-dependencies]
-dev = [
-    "pytest",
-    "pytest-cov", # Used to report total code coverage
-    "pre-commit", # Used to run checks before finalizing a git commit
-    "sphinx>=7.0.0,<8", # Used to automatically generate documentation
-    "sphinx_rtd_theme>=1.2.0,<2", # Used to render documentation
-    "sphinx-autoapi>=3.0.0,<4", # Used to automatically generate api documentation
-    "pylint", # Used for static linting of files
-    # if you add dependencies here while experimenting in a notebook and you
-    # want that notebook to render in your documentation, please add the
-    # dependencies to ./docs/requirements.txt as well.
-    "ipykernel", # Support for Jupyter notebooks
-    "nbconvert", # Needed for pre-commit check to clear output from Python notebooks
-    "nbsphinx", # Used to integrate Python notebooks into Sphinx documentation
-    "ipython", # Also used in building notebooks into Sphinx
-    "jupyterlab",
-    "matplotlib", # Used in sample notebook intro_notebook.ipynb
-]
 
 [build-system]
 requires = [
@@ -64,3 +30,7 @@ build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 write_to = "src/pzserver/_version.py"
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
+optional-dependencies = {dev = { file = ["requirements-dev.txt"] }}

requirements-dev.txt

@@ -0,0 +1,13 @@
+pytest
+pytest-cov
+pre-commit
+sphinx>=7.0.0,<8
+sphinx_rtd_theme>=1.2.0,<2
+sphinx-autoapi>=3.0.0,<4
+pylint
+ipykernel
+nbconvert
+nbsphinx
+ipython
+jupyterlab
+matplotlib

requirements.txt

@@ -0,0 +1,11 @@
+deprecated
+numpy>=1.23
+pandas>=1.2.0
+requests>=2.23.0
+astropy>=5.0.0
+matplotlib>=3.6.0
+tables_io>=0.7.9
+Jinja2>=3.1.2
+ipython>=8.5.0
+h5py>=3.8.0
+pyarrow>=15.0.2