Merge pull request #60 from astronomy-commons/delucchi/copier

Updating to template v1.3.0

Author: delucchi-cmu

.copier-answers.yml

@@ -1,10 +1,15 @@
 # Changes here will be overwritten by Copier
-_commit: v1.2.1
+_commit: v1.3.0
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: lincc-frameworks-team@lists.lsst.org
 author_name: LINCC Frameworks
 create_example_module: false
+custom_install: true
+include_notebooks: false
 module_name: hipscat
+mypy_type_checking: basic
 preferred_linter: pylint
+project_license: BSD
 project_name: hipscat
+use_gitlfs: none
 use_isort: true

.github/workflows/linting.yml

@@ -28,5 +28,5 @@ jobs:
     - name: Analyze code with linter
 
       run: |
-        pylint -rn -sn --recursive=y ./src
+        pylint -rn -sn --recursive=y ./src --rcfile=./src/.pylintrc
 

.github/workflows/publish-to-pypi.yml

@@ -23,7 +23,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

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

@@ -34,4 +34,7 @@ jobs:
       run: |
         python -m pytest tests --cov=hipscat --cov-report=xml
     - name: Upload coverage report to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v3
+    - name: Build docs
+      run: |
+        sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html

.gitignore

@@ -134,4 +134,7 @@ dmypy.json
 .vscode/
 
 # dask
-dask-worker-space/
+dask-worker-space/
+
+# tmp directory
+tmp/

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
       - id: pytest-check
         name: pytest-check
         description: Run unit tests with pytest.
-        entry: python -m pytest --cov=./src --cov-report=html
+        entry: bash -c "if python -m pytest --co -qq; then python -m pytest --cov=./src --cov-report=html; fi"
         language: system
         pass_filenames: false
         always_run: true
@@ -33,6 +33,10 @@ repos:
       - id: no-commit-to-branch
         name: Don't commit to main or master branch
         description: Prevent the user from committing directly to the primary branch.
+      - id: check-added-large-files
+        name: Check for large files
+        description: Prevent the user from committing very large files.
+        args: ['--maxkb=500']
 
     # verify that pyproject.toml is well formed
   - repo: https://github.com/abravalheri/validate-pyproject
@@ -53,21 +57,55 @@ repos:
         files: ^(src|tests)/
 
 
-    # Analyze the code style and report code that doesn't adhere.
+      # Analyze the src code style and report code that doesn't adhere.
   - repo: local
     hooks:
       - id: pylint
-        name: pylint (python files in src/ and tests/)
+        name: pylint (python files in src/)
         entry: pylint
         language: system
         types: [python]
-        files: ^(src|tests)/
+        files: ^src/
+        args:
+          [
+            "-rn", # Only display messages
+            "-sn", # Don't display the score
+            "--rcfile=src/.pylintrc",
+          ]
+    # Analyze the tests code style and report code that doesn't adhere.
+  - repo: local
+    hooks:
+      - id: pylint
+        name: pylint (python files in tests/)
+        entry: pylint
+        language: system
+        types: [python]
+        files: ^tests/
         args:
           [
             "-rn", # Only display messages
             "-sn", # Don't display the score
+            "--rcfile=tests/.pylintrc",
+          ]
+
+
+    # Analyze type hints and report errors.
+  - repo: local
+    hooks:
+      - id: mypy
+        name: mypy (python files in src/ and tests/)
+        entry: mypy
+        language: system
+        types: [python]
+        files: ^(src|tests)/
+        args:
+          [
+          
+            "--ignore-missing-imports", # Ignore imports without type hints
+          
           ]
 
+    # Make sure Sphinx can build the documentation without issues.
   - repo: local
     hooks:
       - id: sphinx-build

.readthedocs.yml

@@ -1,4 +1,4 @@
-# .readthedocs.yaml
+# .readthedocs.yml
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 

LICENSE

@@ -25,4 +25,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

docs/Makefile

@@ -1,21 +1,31 @@
-# Minimal makefile for Sphinx documentation
+# Makefile for Sphinx documentation
 #
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
 SPHINXOPTS    ?= -T -E -d _build/doctrees -D language=en
+EXCLUDENB 	  ?= -D exclude_patterns="notebooks/*"
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = ../_readthedocs/
 
+.PHONY: help no-nb no-notebooks clean Makefile
+
 # Put it first so that "make" without argument is like "make help".
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-.PHONY: help Makefile
+# Build all Sphinx docs locally, except the notebooks
+no-nb no-notebooks:
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(EXCLUDENB) $(O)
+
+# Cleans up files generated by the build process
+clean:
+	rm -r "_build/doctrees"
+	rm -r "$(BUILDDIR)"
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-	
+

docs/conf.py

@@ -31,24 +31,18 @@
 extensions.append("autoapi.extension")
 
 templates_path = []
-exclude_patterns = []
+exclude_patterns = ["_build", "**.ipynb_checkpoints"]
 
-master_doc = "index"  # This assumes that sphinx-build is called from the root directory
-html_show_sourcelink = (
-    False  # Remove 'view source code' from top of page (for html, not python)
-)
-add_module_names = False  # Remove namespaces from class/method signatures
+# This assumes that sphinx-build is called from the root directory
+master_doc = "index"
+# Remove 'view source code' from top of page (for html, not python)
+html_show_sourcelink = False
+# Remove namespaces from class/method signatures
+add_module_names = False
 
 autoapi_type = "python"
 autoapi_dirs = ["../src"]
 autoapi_add_toc_tree_entry = False
 autoapi_member_order = "bysource"
 
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
 html_theme = "sphinx_rtd_theme"
-html_sidebars = {
-    "**": ["globaltoc.html", "relations.html", "searchbox.html"],
-}
-html_css_files = ["readthedocs-custom.css"]  # Override some CSS settings