Merge pull request #365 from FlorianPfaff/pytorch-backend

Can now change backend to pytorch

.github/workflows/mega-linter.yml

@@ -57,7 +57,6 @@ jobs:
           key: ${{ runner.os }}-alpine-wheels-${{ hashFiles('requirements-dev.txt') }}
           restore-keys: |
             ${{ runner.os }}-alpine-wheels-${{ hashFiles('requirements-dev.txt') }}
-
       - name: Set up Alpine Linux
         if: steps.cache-wheels.outputs.cache-hit != 'true'
         uses: jirutka/setup-alpine@v1
@@ -76,7 +75,6 @@ jobs:
             py3-pkgconfig
             curl-dev
             zlib-dev
-
       - name: List workspace
         run: ls -l .
 
@@ -93,6 +91,12 @@ jobs:
           sed 's/==.*//' requirements-dev.txt > requirements-dev_no_version.txt
         shell: alpine.sh {0}
 
+      - name: Remove torch entry (unsupported by alpine)
+        if: steps.cache-wheels.outputs.cache-hit != 'true'
+        run: |
+          sed -i '/^torch/d' requirements-dev_no_version.txt
+        shell: alpine.sh {0}
+
       - name: Run CMake to find LAPACK
         if: steps.cache-wheels.outputs.cache-hit != 'true'
         run: |
@@ -186,7 +190,6 @@ jobs:
           path: |
             megalinter-reports
             mega-linter.log
-
       # Create Pull Request step
       - name: Create Pull Request with applied fixes
         id: cpr
@@ -206,7 +209,6 @@ jobs:
         run: |
           echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
           echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"
-
       # Push new commit if applicable (for now works only on PR from same repository, not from forks)
       - name: Prepare commit
         if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'commit' && github.ref != 'refs/heads/main' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix')

.github/workflows/tests.yml

@@ -27,25 +27,41 @@ jobs:
 
       - name: Install dependencies
         run: |
+          export CUDA_VISIBLE_DEVICES=""
           python -m pip install --upgrade pip
           python -m pip install poetry
-          poetry install --extras healpy_support
+          poetry env use python
+          poetry install --extras "healpy_support" --extras "pytorch_support"
+          poetry run python -m pip install torch==2.1.0+cpu torchaudio==2.1.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
 
       - name: List files and check Python and package versions
         run: |
-          ls -al
-          python -c 'import sys; print(sys.version_info[:])'
-          python -m pip freeze
+          poetry env use python
+          poetry run python -c 'import sys; print(sys.version_info[:])'
+          poetry run python -m pip freeze
+          poetry run python -c "import torch; print(torch.version.cuda)"
+
+      - name: Run tests with numpy backend
+        run: |
+          poetry env use python
+          export PYRECEST_BACKEND=numpy
+          poetry run python -m pytest --rootdir . -v --strict-config --junitxml=junit_test_results_numpy.xml ./pyrecest
+        env:
+          PYTHONPATH: ${{ github.workspace }}
 
-      - name: Run tests
+      - name: Run tests with pytorch backend
+        if: always()
         run: |
           poetry env use python
-          poetry run python -m pytest --rootdir . -v --strict-config --junitxml=junit_test_results.xml ./pyrecest
+          export PYRECEST_BACKEND=pytorch
+          poetry run python -m pytest --rootdir . -v --strict-config --junitxml=junit_test_results_pytorch.xml ./pyrecest
         env:
           PYTHONPATH: ${{ github.workspace }}
 
       - name: Publish test results
         if: always()
         uses: EnricoMi/publish-unit-test-result-action@v2
         with:
-          files: junit_test_results.xml
+          files: |
+            junit_test_results_numpy.xml
+            junit_test_results_pytorch.xml

.github/workflows/update-requirements.yml

@@ -35,7 +35,7 @@ jobs:
         run: python -m poetry update
 
       - name: Update requirements.txt
-        run: python -m poetry export --format requirements.txt --output requirements.txt --extras healpy_support --without-hashes
+        run: python -m poetry export --format requirements.txt --output requirements.txt --extras healpy_support --extras pytorch_support --without-hashes
 
       - name: Update requirements-dev.txt
         run: python -m poetry export --with dev --format requirements.txt --output requirements-dev.txt --without-hashes

.jscpd.json

@@ -0,0 +1,5 @@
+{
+    "ignore": [
+      "pyrecest/_backend/**"
+    ]
+}

.mega-linter.yml

@@ -13,3 +13,5 @@ DISABLE_LINTERS:
   - JSON_JSONLINT # Disable because there is only .devcontainer.json, for which it throws an unwanted warning
   - MAKEFILE_CHECKMAKE # Not using a Makefile
   - SPELL_LYCHEE # Takes pretty long
+
+FILTER_REGEX_EXCLUDE: "pyrecest/_backend/*"

.pylintrc

@@ -63,7 +63,7 @@ ignore-patterns=^\.#
 # (useful for modules/projects where namespaces are manipulated during runtime
 # and thus existing member attributes cannot be deduced by static analysis). It
 # supports qualified module names, as well as Unix pattern matching.
-ignored-modules=
+ignored-modules=pyrecest.backend
 
 # Python code to execute, usually for sys.path manipulation such as
 # pygtk.require().

README.md

@@ -2,7 +2,7 @@
 
 *Recursive Bayesian Estimation for Python*
 
-pyRecEst is a Python library designed for recursive Bayesian estimation. It is currently unstable and lacks a lot of features. Use with caution.
+pyRecEst is a Python library designed for recursive Bayesian estimation, which supports numpy and pytorch as backends. It is currently unstable and lacks a lot of features. Use with caution.
 
 ## Usage
 
@@ -12,7 +12,7 @@ Please refer to the test cases for usage examples.
 
 - Florian Pfaff (<pfaff@kit.edu>)
 
-pyRecEst borrows its structure from libDirectional and follows its code closely for many classes. libDirectional, a project to which I contributed extensively, is [available on GitHub](https://github.com/libDirectional).
+pyRecEst borrows its structure from libDirectional and follows its code closely for many classes. libDirectional, a project to which I contributed extensively, is [available on GitHub](https://github.com/libDirectional). The backend implementations are based on those of [geomstats](https://github.com/geomstats/geomstats).
 
 ## License
 `pyRecEst` is licensed under the MIT License.