Merge pull request #134 from FlorianPfaff/megalinter-v7.3.0

Upped mega linter to v7.3.0

.github/workflows/mega-linter.yml

@@ -115,7 +115,6 @@ jobs:
               cd ..
               mv SHTOOLS/dist/*.whl ./alpine-wheels/
               rm -rf SHTOOLS
-              rm -rf CMakeFiles
             elif ! pip download --only-binary=:all: --no-deps "$package" -d ./alpine-wheels > /dev/null 2>&1; then
               echo "No compatible wheel for $package found, building..."
               pip wheel --wheel-dir=./alpine-wheels "$package"
@@ -128,25 +127,22 @@ jobs:
       - name: List available wheels
         run: ls -l ./alpine-wheels
 
+      - name: Clean up temporary files (in case they are generated)
+        run: rm -rf CMakeFiles CMakeCache.txt cmake_install.cmake Makefile
+
       # MegaLinter
       - name: MegaLinter
         id: ml
         # You can override MegaLinter flavor used to have faster performances
-        # More info at https://megalinter.io/flavors/
-        uses: oxsecurity/megalinter/flavors/python@v7.1.0
+        # More info at https://megalinter.io/latest/configuration/#shared-variables
+        uses: oxsecurity/megalinter/flavors/python@v7.3.0
         env:
           # All available variables are described in documentation
-          # https://megalinter.io/configuration/
-          VALIDATE_ALL_CODEBASE: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} # Validates all source when push on main, else just the git diff with main. Override with true if you always want to lint all sources
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          # https://megalinter.io/latest/configuration/#shared-variables
           # ADD YOUR CUSTOM ENV VARIABLES HERE OR DEFINE THEM IN A FILE .mega-linter.yml AT THE ROOT OF YOUR REPOSITORY
-          # DISABLE: COPYPASTE,SPELL # Uncomment to disable copy-paste and spell checks
-        #with:
-        #  args: -v ${{ github.workspace }}/cache-directory:/cache-directory
-
-      #- name: List cache-directory contents
-      #  if: ${{ success() }} || ${{ failure() }}
-      #  run: ls -la ${{ github.workspace }}/cache-directory
+          VALIDATE_ALL_CODEBASE: true #  ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} # Validates all source when push on main, else just the git diff with main. Override with true if you always want to lint all sources
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          EMAIL_REPORTER_SMTP_PASSWORD: ${{ secrets.SMTP_PASSWORD }}
 
       # Upload MegaLinter artifacts
       - name: Archive production artifacts
@@ -161,25 +157,25 @@ jobs:
       # Create pull request if applicable (for now works only on PR from same repository, not from forks)
       - name: Create Pull Request with applied fixes
         id: cpr
-        if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'pull_request' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository)
+        if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'pull_request' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix')
         uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ secrets.PAT || secrets.GITHUB_TOKEN }}
           commit-message: "[MegaLinter] Apply linters automatic fixes"
           title: "[MegaLinter] Apply linters automatic fixes"
           labels: bot
       - name: Create PR output
-        if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'pull_request' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository)
+        if: steps.ml.outputs.has_updated_sources == 1 && (env.APPLY_FIXES_EVENT == 'all' || env.APPLY_FIXES_EVENT == github.event_name) && env.APPLY_FIXES_MODE == 'pull_request' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name == github.repository) && !contains(github.event.head_commit.message, 'skip fix')
         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)
+        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')
         run: sudo chown -Rc $UID .git/
       - name: Commit and push applied linter fixes
-        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)
+        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')
         uses: stefanzweifel/git-auto-commit-action@v4
         with:
           branch: ${{ github.event.pull_request.head.ref || github.head_ref || github.ref }}

.github/workflows/update-requirements.yml

@@ -1,3 +1,4 @@
+---
 name: Update requirements.txt
 
 permissions:

.mega-linter.yml

@@ -12,3 +12,4 @@ DISABLE_LINTERS:
   - REPOSITORY_TRIVY # Reenable as soon as (if?) https://avd.aquasec.com/nvd/2021/cve-2021-29063/ confirms that 1.3.0 is no longer a risk
   - JSON_JSONLINT # Disable because there is only .devcontainer.json, for which it throws an unwanted warning
   - MAKEFILE_CHECKMAKE # Not using a Makefile
+  - REPOSITORY_GRYPE # Currently, a false alarm is raised

README.md

@@ -10,7 +10,7 @@ Please refer to the test cases for usage examples.
 
 ## Credits
 
-- Florian Pfaff ([email protected])
+- Florian Pfaff (<[email protected]>)
 
 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/distributions/hypertorus/custom_toroidal_distribution.py

@@ -1,7 +1,10 @@
-from .custom_hypertoroidal_distribution import CustomHypertoroidalDistribution
 from .abstract_toroidal_distribution import AbstractToroidalDistribution
+from .custom_hypertoroidal_distribution import CustomHypertoroidalDistribution
+
 
-class CustomToroidalDistribution(CustomHypertoroidalDistribution, AbstractToroidalDistribution):
+class CustomToroidalDistribution(
+    CustomHypertoroidalDistribution, AbstractToroidalDistribution
+):
     def __init__(self, f):
         AbstractToroidalDistribution.__init__(self)
-        CustomHypertoroidalDistribution.__init__(self, f, 2)
+        CustomHypertoroidalDistribution.__init__(self, f, 2)

pyrecest/distributions/hypertorus/toroidal_von_mises_sine_distribution.py

@@ -21,7 +21,13 @@ def __init__(self, mu, kappa, lambda_):
     @property
     def norm_const(self):
         def s(m):
-            return comb(2 * m, m) * (self.lambda_ ** 2 / 4 / self.kappa[0] / self.kappa[1]) ** m * iv(m, self.kappa[0]) * iv(m, self.kappa[1])
+            return (
+                comb(2 * m, m)
+                * (self.lambda_**2 / 4 / self.kappa[0] / self.kappa[1]) ** m
+                * iv(m, self.kappa[0])
+                * iv(m, self.kappa[1])
+            )
+
         Cinv = 4 * np.pi**2 * np.sum([s(m) for m in range(11)])
         return Cinv
 

pyrecest/distributions/nonperiodic/gaussian_distribution.py

@@ -73,7 +73,7 @@ def convolve(self, other):
         return GaussianDistribution(new_mu, new_C, check_validity=False)
 
     def marginalize_out(self, dimensions):
-        if type(dimensions) is int:  # Make it iterable if single integer
+        if isinstance(dimensions, int):  # Make it iterable if single integer
             dimensions = [dimensions]
         assert all(dim <= self.dim for dim in dimensions)
         remaining_dims = [i for i in range(self.dim) if i not in dimensions]

pyrecest/tests/distributions/test_hypercylindrical_dirac_distribution.py

@@ -56,8 +56,10 @@ def test_reweigh(self):
         # Define functions for testing
         def f1(x):
             return np.sum(x, axis=-1) == 3
+
         def f2(x):
             return 2 * np.ones(x.shape[0])
+
         def f3(x):
             return x[:, 0]
 

pyrecest/tests/distributions/test_wrapped_laplace_distribution.py

@@ -28,6 +28,7 @@ def laplace(x):
 
         def pdftemp(x):
             return sum(laplace(z) for z in x + 2 * np.pi * np.arange(-20, 21))
+
         for x in [0, 1, 2, 3, 4]:
             np.testing.assert_allclose(self.wl.pdf(x), pdftemp(x), rtol=1e-10)