Refactor the repository to make it simpler (#55)

Ditch the eql_source_layouts package: remove MANIFEST.in, setup.py and
versioneer. Move all code inside the notebooks folder. All additional code
lives inside notebooks/source_layouts, including its test functions. Replace
os.path for pathlib. Add a new run target in the Makefile. Save
variables into JSON files and create a notebook to convert them all to LaTeX
variables. Prevent saving & loading the datasets in the same notebook. Remove
setup.cfg, move flake8 configuration to .flake8 and don't ignore F401
anymore. Add flake8-bugbear as a dependency.

.flake8

@@ -0,0 +1,8 @@
+[flake8]
+ignore = E203, E266, E501, W503, E741
+max-line-length = 88
+exclude = notebooks/.ipynb_checkpoints
+per-file-ignores =
+ # imported but unused
+ __init__.py: F401
+

.github/workflows/test.yml

@@ -31,5 +31,4 @@ jobs:
  - name: Test with pytest
  run: |
  pip install pytest pytest-cov coverage
- pip install -e .
  make test

Makefile

@@ -1,28 +1,33 @@
-# Build, package, test, and clean
-PROJECT=eql_source_layouts
-TESTDIR=tmp-test-dir-with-unique-name
-PYTEST_ARGS=--cov-config=../.coveragerc --cov-report=term-missing --cov=$(PROJECT) --doctest-modules -v --pyargs
-NUMBATEST_ARGS=--doctest-modules -v --pyargs -m use_numba
-LINT_FILES=setup.py $(PROJECT)
-BLACK_FILES=setup.py $(PROJECT) notebooks
-FLAKE8_FILES=setup.py $(PROJECT) notebooks
+# Check styling and test notebooks and extra code
+NOTEBOOKS=notebooks
+PYTEST_ARGS=--cov --cov-report=term-missing --cov -v
+LINT_FILES=$(NOTEBOOKS)
+BLACK_FILES=$(NOTEBOOKS)
+FLAKE8_FILES=$(NOTEBOOKS)
+JUPYTEXT=jupytext --execute --set-kernel - --to notebook
 
 help:
  @echo "Commands:"
  @echo ""
+ @echo " run run every notebook on the repository"
  @echo " test run the test suite and report coverage"
  @echo " format run black to automatically format the code"
  @echo " check run code style and quality checks (black and flake8)"
  @echo " lint run pylint for a deeper (and slower) quality check"
  @echo " clean clean up build and generated files"
+ @echo " sync make jupytext to sync notebooks and scripts"
  @echo ""
 
+
+run:
+ $(JUPYTEXT) $(NOTEBOOKS)/*.py
+
+sync:
+ jupytext --to notebook --set-kernel - $(NOTEBOOKS)/*.py
+
 test:
  # Run a tmp folder to make sure the tests are run on the installed version
- mkdir -p $(TESTDIR)
- cd $(TESTDIR); MPLBACKEND='agg' pytest $(PYTEST_ARGS) $(PROJECT)
- cp $(TESTDIR)/.coverage* .
- rm -rvf $(TESTDIR)
+ MPLBACKEND='agg' pytest $(PYTEST_ARGS) $(NOTEBOOKS)
 
 format:
  black $(BLACK_FILES)
@@ -37,5 +42,5 @@ lint:
 clean:
  find . -name "*.pyc" -exec rm -v {} \;
  find . -name ".coverage.*" -exec rm -v {} \;
- rm -rvf build dist MANIFEST *.egg-info __pycache__ .coverage .cache .pytest_cache
- rm -rvf $(TESTDIR) dask-worker-space
+ rm -rvf build dist *.egg-info __pycache__ .coverage .cache .pytest_cache
+ rm -rvf dask-worker-space

environment.yml

@@ -20,6 +20,4 @@ dependencies:
  - black
  - pylint
  - flake8
- # Install our package in editable mode
- - pip:
- - -e .
+ - flake8-bugbear