Updating testing and docs infrastructure (#392)

* adding tox and updating some deps

* removing 3.7 tests for numpy

* notebooks

* adding notebook output

* adding binder config

* adding tqdm to binder requirements

* using binder conda env

* conda env issue

* conda binder install local

.github/workflows/tests.yml

@@ -2,133 +2,116 @@ name: Tests
 
 on:
   push:
-    branches: [ main ]
+    branches:
+      - main
+    tags:
+      - "*"
+    paths-ignore:
+      - "joss/**"
+      - "docs/**"
   pull_request:
-    branches: [ main ]
-  release:
-    types: [ published ]
-
+
 jobs:
   tests:
-    name: "py${{ matrix.python-version }} / ${{ matrix.os }} / extras: ${{ matrix.extras }}"
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9"]
-        extras: [true]
+        python-version: ["3.7", "3.8", "3.9"]
         os: ["ubuntu-latest"]
         include:
           - python-version: "3.8"
-            extras: false
-            os: "ubuntu-latest"
-          - python-version: "3.8"
-            extras: true
             os: "macos-latest"
           - python-version: "3.8"
-            extras: true
             os: "windows-latest"
 
     steps:
-    - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      if: ${{ matrix.extras }}
-      run: |
-        python -m pip install -U pip
-        python -m pip install -e ".[extras,tests]"
-    - name: Install dependencies without extras
-      if: ${{ !matrix.extras }}
-      run: |
-        python -m pip install -U pip
-        python -m pip install -e ".[tests]"
-    - name: Run tests
-      run: |
-        python -m pytest -v src/emcee/tests --cov emcee
-    - name: Get unique id
-      if: ${{ matrix.os != 'windows-latest' }}
-      id: unique-id
-      env:
-        STRATEGY_CONTEXT: ${{ toJson(strategy) }}
-      run: |
-        export JOB_ID=`echo $STRATEGY_CONTEXT | md5sum`
-        echo "::set-output name=id::$JOB_ID"
-    - uses: actions/upload-artifact@v2
-      if: ${{ matrix.os != 'windows-latest' }}
-      with:
-        name: cov-${{ steps.unique-id.outputs.id }}
-        path: .coverage
-
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install -U coveralls coverage[toml] tox tox-gh-actions
+      - name: Run tests
+        run: python -m tox
+      - name: Combine and upload coverage
+        run: |
+          python -m coverage combine
+          python -m coverage xml -i
+          python -m coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COVERALLS_PARALLEL: true
+          COVERALLS_FLAG_NAME: ${{ matrix.python-version }}-${{ matrix.os }}
+
   coverage:
-    name: "Merge and upload coverage"
     needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.9"
+      - name: Finish coverage collection
+        run: |
+          python -m pip install -U pip
+          python -m pip install -U coveralls
+          python -m coveralls --finish
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  lint:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0
-      - name: Set up Python
+      - name: Setup Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
-      - name: Download all artifacts
-        uses: actions/download-artifact@v2
-      - name: Merge and upload coverage
+          python-version: "3.9"
+      - name: Install dependencies
         run: |
-          python -m pip install coveralls
-          find . -name \.coverage -exec coverage combine --append {} \;
-          coveralls
-        env:
-          GITHUB_TOKEN: ${{ secrets.github_token }}
+          python -m pip install -U pip
+          python -m pip install tox
+      - name: Lint the code
+        run: python -m tox -e lint
 
   build:
-    name: Build source distribution
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0
-          submodules: true
-
       - uses: actions/setup-python@v2
         name: Install Python
         with:
-          python-version: "3.8"
-
-      - name: Build
-        run: |
-          python -m pip install -U pip pep517 twine setuptools_scm
-          python -m pep517.build .
-      - name: Test the sdist
+          python-version: "3.9"
+      - name: Build sdist and wheel
         run: |
-          python -m venv venv-sdist
-          venv-sdist/bin/python -m pip install dist/emcee*.tar.gz
-          venv-sdist/bin/python -c "import emcee;print(emcee.__version__)"
-      - name: Test the wheel
-        run: |
-          python -m venv venv-wheel
-          venv-wheel/bin/python -m pip install dist/emcee*.whl
-          venv-wheel/bin/python -c "import emcee;print(emcee.__version__)"
+          python -m pip install -U pip
+          python -m pip install -U build
+          python -m build .
       - uses: actions/upload-artifact@v2
         with:
-          name: dist
           path: dist/*
 
   upload_pypi:
-    needs: [tests, build]
+    needs: [tests, lint, build]
     runs-on: ubuntu-latest
-    if: github.event_name == 'release' && github.event.action == 'published'
+    if: startsWith(github.ref, 'refs/tags/')
     steps:
       - uses: actions/download-artifact@v2
         with:
-          name: dist
+          name: artifact
           path: dist
-      - uses: pypa/gh-action-pypi-publish@master
+
+      - uses: pypa/[email protected]
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}
-          # To test: repository_url: https://test.pypi.org/legacy/

.gitignore

@@ -21,3 +21,4 @@ emcee_version.py
 
 .tox
 env
+.eggs

.pre-commit-config.yaml

@@ -1,29 +1,26 @@
+
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v2.3.0
+  rev: v4.0.1
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
   - id: debug-statements
 
-- repo: https://github.com/asottile/seed-isort-config
-  rev: v1.9.2
-  hooks:
-  - id: seed-isort-config
-    args: [--application-directories=src]
-
-- repo: https://github.com/pre-commit/mirrors-isort
-  rev: v4.3.20
+- repo: https://github.com/PyCQA/isort
+  rev: "5.9.1"
   hooks:
   - id: isort
     args: []
+    additional_dependencies: [toml]
+    exclude: docs/tutorials
 
 - repo: https://github.com/psf/black
-  rev: 19.3b0
+  rev: "21.6b0"
   hooks:
   - id: black
 
 - repo: https://github.com/dfm/black_nbconvert
-  rev: master
+  rev: v0.2.0
   hooks:
   - id: black_nbconvert

AUTHORS.rst

@@ -1 +1 @@
-The list of contributors can be found `on GitHub <https://github.com/dfm/emcee/graphs/contributors>`_.
+The list of contributors can be found `on GitHub <https://github.com/dfm/emcee/graphs/contributors>`_.

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2010-2019 Daniel Foreman-Mackey & contributors.
+Copyright (c) 2010-2021 Daniel Foreman-Mackey & contributors.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -35,9 +35,7 @@ Attribution
 
 Please cite `Foreman-Mackey, Hogg, Lang & Goodman (2012)
 <https://arxiv.org/abs/1202.3665>`_ if you find this code useful in your
-research and add your paper to `the testimonials list
-<https://github.com/dfm/emcee/blob/master/docs/testimonials.rst>`_.
-The BibTeX entry for the paper is::
+research. The BibTeX entry for the paper is::
 
     @article{emcee,
        author = {{Foreman-Mackey}, D. and {Hogg}, D.~W. and {Lang}, D. and {Goodman}, J.},
@@ -53,7 +51,7 @@ The BibTeX entry for the paper is::
 License
 -------
 
-Copyright 2010-2019 Dan Foreman-Mackey and contributors.
+Copyright 2010-2021 Dan Foreman-Mackey and contributors.
 
 emcee is free software made available under the MIT License. For details see
 the LICENSE file.

VISION.md

@@ -1,4 +1,3 @@
 - Easy to use gradient-free MCMC sampling of black box log probability functions
 - Few bells and whistles: no plotting, no modeling, no marginal likelihood calculation, etc.
 - Any sampling algorithm must have published proof of correctness
-

binder/environment.yml

@@ -0,0 +1,18 @@
+name: emcee
+channels:
+  - conda-forge
+dependencies:
+  - python
+  - numpy
+  - scipy
+  - h5py
+  - matplotlib
+  - corner
+  - tqdm
+  - mpi4py
+  - schwimmbad
+  - pip
+  - pip:
+    - celerite
+    - autograd
+    - ..