Merge pull request #85 from OpenSourceEconomics/debug_workflow

Debugging workflow: rearrange dependencies; bump rpy2 version; use mamba

.github/workflows/continuous-integration-workflow.yml

@@ -6,6 +6,9 @@ jobs:
   run-tests:
     name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
 
     strategy:
       fail-fast: false
@@ -19,32 +22,33 @@ jobs:
     - uses: conda-incubator/setup-miniconda@v2
       with:
           auto-update-conda: false
+          mamba-version: "*"
           activate-environment: econsa
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
 
+    # Dear fellow dev:
+    # Please keep this step in the CI as long as we still use conda.
+    # If you are not debugging, just comment them out.
+    # - name: (Debug) Check system status.
+    #   run: |
+    #     conda info
+    #     conda config --show-sources
+    #     # printenv | sort
+
     - name: Run test suite.
-      shell: bash -l {0}
       run: |
         pytest --cov=econsa --cov-report=xml
 
     - name: Run figures.
       if: runner.os == 'Linux'
-      shell: bash -l {0}
       run: |
         export PATH="$PATH:/usr/share/miniconda/bin"
         source .envrc
         run-figures
 
     - name: Upload coverage to Codecov.
-      if: runner.os == 'Linux' && matrix.python-version == '3.7'
+      if: runner.os == 'Linux' && matrix.python-version == '3.9'
       uses: codecov/codecov-action@v1
       with:
         file: coverage.xml
-
-    - name: Run pre-commits.
-      if: runner.os == 'Linux'
-      shell: bash -l {0}
-      run: |
-        pre-commit install
-        pre-commit run --all-files

.pre-commit-config.yaml

@@ -24,7 +24,7 @@ repos:
     -   id: black
         args: ['--line-length=100']
         files: '(\.pyi?|wscript|ipynb)$'
-        language_version: python3.7
+        language_version: python3
         additional_dependencies: [black-nb]
 -   repo: https://gitlab.com/pycqa/flake8
     rev: 3.8.3

configurations/rtd_environment.yml

@@ -1,42 +1,43 @@
 name: econsa
 
 channels:
-  - defaults
   - conda-forge
+  - defaults
   - opensourceeconomics
 
 dependencies:
-  - python=3.7
-  - sphinx
-  - pandas
-  - numpy=1.18
+  - python
   - pip
+
+  - pandas
+  - numpy<1.20
+  - numpoly<1.2.0
   - scipy
   - statsmodels
-  - jupyter
-  - jupyterlab
+  - matplotlib-base
   - seaborn
   - numba
-  - pdbpp
   - temfpy>=1.1
   - chaospy
+
+  - ipykernel
+
   - pytest
   - pytest-black
   - pytest-flake8
   - pytest-cov
   - pytest-sugar
   - black
   - hypothesis
+
+  - sphinx
   - nbsphinx
+  - numpydoc
   - sphinx_rtd_theme
-  - sphinxcontrib-bibtex<2.0.0
-  - pre-commit
+  - sphinxcontrib-bibtex>=2.0.0
 
   - pip:
     - pytest-stress
     - pytest-randomly
     - black-nb
     - flake8-nb
-    - numpydoc
-    - cairosvg
-    - sphinxcontrib-svg2pdfconverter[CairoSVG]

docs/source/conf.py

@@ -229,3 +229,6 @@ def setup(app):
 
 # Use new CDN path of MathJax
 mathjax_path = "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
+
+# Set bib file for sphinxcontrib-bibtex
+bibtex_bibfiles = ["bibliography.bib"]

environment.yml

@@ -1,47 +1,54 @@
 name: econsa
 
 channels:
-  - defaults
   - conda-forge
+  - defaults
   - opensourceeconomics
 
 dependencies:
-  - python=3.7
-  - sphinx
-  - pandas
-  - numpy=1.18
+  - python
   - pip
+
+  - pandas
+  - numpy<1.20
+  - numpoly<1.2.0
   - scipy
   - statsmodels
-  - ipykernel
-  - jupyterlab
+  - matplotlib-base
   - seaborn
   - numba
-  - pdbpp
-  - matplotlib-base
   - temfpy>=1.1
   - chaospy
+
+  - ipykernel
+  - jupyterlab
+
   - pre-commit
-  - pytest=5.4.3
+  - pytest
   - pytest-cov
   - pytest-sugar
   - pytest-black
   - pytest-flake8
-  - black>=20.8b0
+  - black
+  - pdbpp
   - hypothesis
+
+  - sphinx
   - nbsphinx
+  - numpydoc
   - sphinx_rtd_theme
-  - sphinxcontrib-bibtex
+  - sphinxcontrib-bibtex>=2.0.0
+
   - r-base
   - r-r.utils
   - r-condmvnorm
-  - rpy2==2.9.4
+  - rpy2
 
   - pip:
+    # Dear fellow dev:
+    # Please check twice before you add anything here
+    # that you absolutely cannot find it with https://anaconda.org/search.
     - pytest-stress
     - pytest-randomly
     - black-nb
     - flake8-nb
-    - numpydoc
-    - cairosvg
-    - sphinxcontrib-svg2pdfconverter[CairoSVG]