Merge pull request #175 from esa/develop

develop -> release for Release 0.4.0

Author: gomezzz

.github/ISSUE_TEMPLATE/release.md

@@ -15,7 +15,7 @@ _to be written during release process_
 ## What Needs to Be Done (chronologically)
 
 - [ ] Create PR from `main` -> `develop` to incorporate hotfixes / documentation changes.
-- [ ] In case of merge conflicts create PR to fix them which is then merged into main.
+- [ ] In case of merge conflicts create PR to fix them which is then merged into main / fix on GitHub but make sure to let it create a new branch for the changes.
 - [ ] Review the PR
 - [ ] Create PR to merge from current develop into release branch
 - [ ] Write Changelog in PR and request review
@@ -25,7 +25,7 @@ _to be written during release process_
 - [ ] Check documentation -> Check presence of documentation for all features by locally building the docs on the release
 - [ ] Change version number in setup.py and docs (under conf.py)
 - [ ] Trigger the Upload Python Package to testpypi GitHub Action (https://github.com/esa/torchquad/actions/workflows/deploy_to_test_pypi.yml) on the release branch (need to be logged in)
-- [ ] Test the build on testpypi
+- [ ] Test the build on testpypi (with `pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple torchquad`)
 - [ ] Finalize release on the release branch
 - [ ] Create PR: release → main , develop -> main
 - [ ] PR Reviews

.github/workflows/autoblack.yml

@@ -18,13 +18,3 @@ jobs:
         run: pip install black
       - name: Run black --check .
         run: black --check .
-      - name: If needed, commit black changes to the pull request
-        if: failure()
-        run: |
-          black .
-          git config --global user.name 'htoftevaag'
-          git config --global user.email '[email protected]'
-          git remote set-url origin https://x-access-token:${{ secrets.Autoblack_access_token }}@github.com/$GITHUB_REPOSITORY
-          git checkout $GITHUB_HEAD_REF
-          git commit -am "WORKFLOW: Format Python code with black"
-          git push

.github/workflows/run_tests.yml

@@ -6,49 +6,69 @@ name: Running tests
 on:
   push:
     branches:
-    - main
-    - develop
+      - main
+      - develop
   pull_request:
   workflow_dispatch:
 jobs:
   lint_flake8:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Lint with flake8
-      run: |
-        pip install flake8
-        flake8 . --count --show-source --statistics
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Lint with flake8
+        run: |
+          pip install flake8
+          flake8 . --count --show-source --statistics
 
   build:
-
     runs-on: ubuntu-latest
-
+    permissions:
+      pull-requests: write
+      contents: read
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Search for severe code errors with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        pip install flake8
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Install dependencies
-      run: |
-        $CONDA/bin/conda env update --file environment_all_backends.yml --name base
-    - name: Test with pytest
-      run: |
-        cd torchquad/tests
-        conda install pytest
-        $CONDA/bin/pip3 install pytest-error-for-skips
-        $CONDA/bin/pytest -ra --error-for-skips
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Search for severe code errors with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          pip install flake8
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+      #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+      #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: provision-with-micromamba
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: environment_all_backends.yml
+          environment-name: torchquad
+          cache-downloads: true
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          micromamba activate torchquad
+          cd torchquad/tests/
+          pip install pytest
+          pip install pytest-error-for-skips
+          pip install pytest-cov
+          pytest -ra --error-for-skips --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=../../torchquad . | tee pytest-coverage.txt
+      - name: pytest coverage comment
+        uses: MishaKav/pytest-coverage-comment@main
+        if: github.event_name == 'pull_request'
+        with:
+          pytest-coverage-path: ./torchquad/tests/pytest-coverage.txt
+          title: Coverage Report
+          badge-title: Overall Coverage
+          hide-badge: false
+          hide-report: false
+          create-new-comment: false
+          hide-comment: false
+          report-only-changed-files: false
+          junitxml-path: ./torchquad/tests/pytest.xml

.gitignore

@@ -129,4 +129,6 @@ dmypy.json
 .pyre/
 
 my_notebooks
-.vscode
+.vscode
+pytest-coverage.txt
+pytest.xml

CITATION.cff

@@ -0,0 +1,57 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: "torchquad: Numerical Integration in Arbitrary
+  Dimensions with PyTorch, TensorFlow & JAX"
+authors:
+  - given-names: Pablo
+    family-names: Gómez
+    email: [email protected]
+    affiliation: >-
+      Advanced Concepts Team, European Space Agency,
+      Noordwijk, The Netherlands
+    orcid: "https://orcid.org/0000-0002-5631-8240"
+  - given-names: Håvard
+    family-names: Hem Toftevaag
+    affiliation: >-
+      Advanced Concepts Team, European Space Agency,
+      Noordwijk, The Netherlands
+    orcid: "http://orcid.org/0000-0003-4692-5722"
+  - given-names: Gabriele
+    family-names: Meoni
+    affiliation: >-
+      Advanced Concepts Team, European Space Agency,
+      Noordwijk, The Netherlands
+    orcid: "http://orcid.org/0000-0001-9311-6392"
+repository-code: "https://github.com/esa/torchquad/"
+url: "https://www.esa.int/gsp/ACT/open_source/torchquad/"
+repository-artifact: "https://anaconda.org/conda-forge/torchquad"
+license: GPL-3.0
+preferred-citation:
+  type: article
+  authors:
+  - given-names: Pablo
+    family-names: Gómez
+    email: [email protected]
+    affiliation: >-
+      Advanced Concepts Team, European Space Agency,
+      Noordwijk, The Netherlands
+    orcid: "https://orcid.org/0000-0002-5631-8240"
+  - given-names: Håvard
+    family-names: Hem Toftevaag
+    affiliation: >-
+      Advanced Concepts Team, European Space Agency,
+      Noordwijk, The Netherlands
+    orcid: "http://orcid.org/0000-0003-4692-5722"
+  - given-names: Gabriele
+    family-names: Meoni
+    affiliation: >-
+      Advanced Concepts Team, European Space Agency,
+      Noordwijk, The Netherlands
+    orcid: "http://orcid.org/0000-0001-9311-6392"
+  doi: "10.21105/joss.03439"
+  journal: "Journal of Open Source Software"
+  title: "torchquad: Numerical Integration in Arbitrary
+  Dimensions with PyTorch"
+  issue: 6
+  volume: 64
+  year: 2021

README.md

@@ -3,7 +3,7 @@
 *** Based on https://github.com/othneildrew/Best-README-Template
 -->
 
-![Read the Docs (version)](https://img.shields.io/readthedocs/torchquad/main?style=flat-square) ![GitHub Workflow Status (branch)](https://img.shields.io/github/workflow/status/esa/torchquad/Running%20tests/main?style=flat-square) ![GitHub last commit](https://img.shields.io/github/last-commit/esa/torchquad?style=flat-square)
+![Read the Docs (version)](https://img.shields.io/readthedocs/torchquad/main?style=flat-square) [![Tests](https://github.com/esa/torchquad/actions/workflows/run_tests.yml/badge.svg)](https://github.com/esa/torchquad/actions/workflows/run_tests.yml) ![GitHub last commit](https://img.shields.io/github/last-commit/esa/torchquad?style=flat-square)
 ![GitHub](https://img.shields.io/github/license/esa/torchquad?style=flat-square) ![Conda (channel only)](https://img.shields.io/conda/vn/conda-forge/torchquad?style=flat-square) ![PyPI](https://img.shields.io/pypi/v/torchquad?style=flat-square) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/torchquad?style=flat-square)
 
 ![GitHub contributors](https://img.shields.io/github/contributors/esa/torchquad?style=flat-square)
@@ -23,8 +23,6 @@
     <a href="https://torchquad.readthedocs.io"><strong>Explore the docs »</strong></a>
     <br />
     <br />
-    <a href="https://github.com/esa/torchquad/blob/master/notebooks/Torchquad%20-%20Example%20notebook.ipynb">View Example notebook</a>
-    ·
     <a href="https://github.com/esa/torchquad/issues">Report Bug</a>
     ·
     <a href="https://github.com/esa/torchquad/issues">Request Feature</a>
@@ -127,7 +125,7 @@ Note also that installing PyTorch with *pip* may **not** set it up with CUDA sup
 Here are installation instructions for other numerical backends:
    ```sh
    conda install "tensorflow>=2.6.0=cuda*" -c conda-forge
-   pip install "jax[cuda]>=0.2.22" --find-links https://storage.googleapis.com/jax-releases/jax_releases.html # linux only
+   pip install "jax[cuda]>=0.2.22" --find-links https://storage.googleapis.com/jax-releases/jax_cuda_releases.html # linux only
    conda install "numpy>=1.19.5" -c conda-forge
    ```
 
@@ -275,7 +273,7 @@ Created by ESA's [Advanced Concepts Team](https://www.esa.int/gsp/ACT/index.html
 
 - Pablo Gómez - `pablo.gomez at esa.int`
 - Gabriele Meoni - `gabriele.meoni at esa.int`
-- Håvard Hem Toftevaag - `havard.hem.toftevaag at esa.int`
+- Håvard Hem Toftevaag
 
 Project Link: [https://github.com/esa/torchquad](https://github.com/esa/torchquad)
 

docs/source/install.rst

@@ -57,7 +57,7 @@ Here are installation instructions for other numerical backends:
    .. code-block:: bash
 
       conda install "tensorflow>=2.6.0=cuda*" -c conda-forge
-      pip install "jax[cuda]>=0.2.22" --find-links https://storage.googleapis.com/jax-releases/jax_releases.html # linux only
+      pip install "jax[cuda]>=0.2.22" --find-links https://storage.googleapis.com/jax-releases/jax_cuda_releases.html # linux only
       conda install "numpy>=1.19.5" -c conda-forge
 
 More installation instructions for numerical backends can be found in

docs/source/integration_methods.rst

@@ -51,3 +51,14 @@ Trapezoid Rule
 .. autoclass:: torchquad.Trapezoid
    :members: integrate
    :noindex:
+
+Gaussian Quadrature
+^^^^^^^^^^^^^^^^^^^^^^
+
+.. autoclass:: torchquad.Gaussian
+   :members: integrate, _resize_roots
+   :noindex:
+
+.. autoclass:: torchquad.GaussLegendre
+   :members: integrate
+   :noindex: