Flake 8 bugs

bioexcel · Jan 8, 2025 · f3c8dd8 · f3c8dd8
1 parent e2b8837
commit f3c8dd8
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Showing 2 changed files with 61 additions and 77 deletions.
diff --git a/.github/workflows/pr-tests.yml b/.github/workflows/pr-tests.yml
@@ -13,60 +13,60 @@ jobs:
         python-version: ["3.10"]
     runs-on: ${{ matrix.os }}
     steps:
-      # - name: Check out repository code
-      #   uses: actions/checkout@v4
+      - name: Check out repository code
+        uses: actions/checkout@v4
 
-      # - run: echo "Repository -> ${{ github.repository }}"
-      # - run: echo "Branch -> ${{ github.ref }}"
-      # - run: echo "Trigger event -> ${{ github.event_name }}"
-      # - run: echo "Runner OS -> ${{ runner.os }}"
+      - run: echo "Repository -> ${{ github.repository }}"
+      - run: echo "Branch -> ${{ github.ref }}"
+      - run: echo "Trigger event -> ${{ github.event_name }}"
+      - run: echo "Runner OS -> ${{ runner.os }}"
 
-      # - name: List files in the repository
-      #   run: |
-      #     ls ${{ github.workspace }}
+      - name: List files in the repository
+        run: |
+          ls ${{ github.workspace }}
 
-      # - name: Remove all micromamba installations
-      #   run: |
-      #     rm -rf $HOME/.bash_profile $HOME/.conda $HOME/micromamba $HOME/micromamba-bin 2>/dev/null
-      #     touch $HOME/.bash_profile
+      - name: Remove all micromamba installations
+        run: |
+          rm -rf $HOME/.bash_profile $HOME/.conda $HOME/micromamba $HOME/micromamba-bin 2>/dev/null
+          touch $HOME/.bash_profile
 
-      # - name: setup-micromamba
-      #   uses: mamba-org/[email protected]
-      #   with:
-      #     generate-run-shell: true
-      #     micromamba-version: '2.0.2-2'
-      #     post-cleanup: 'all'
-      #     init-shell: bash
-      #     environment-file: .github/env.yaml
-      #     create-args: >-
-      #       python=${{ matrix.python-version }}
-      #       pytest
-      #       pytest-cov
-      #       pytest-html
-      #       flake8
-      #       pip
+      - name: setup-micromamba
+        uses: mamba-org/[email protected]
+        with:
+          generate-run-shell: true
+          micromamba-version: '2.0.2-2'
+          post-cleanup: 'all'
+          init-shell: bash
+          environment-file: .github/env.yaml
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pytest
+            pytest-cov
+            pytest-html
+            flake8
+            pip
 
-      # - name: List installed package versions
-      #   shell: bash -l {0}
-      #   run: micromamba list
+      - name: List installed package versions
+        shell: bash -l {0}
+        run: micromamba list
 
-      # - name: Checkout biobb_common
-      #   uses: actions/checkout@v4
-      #   with:
-      #     repository: bioexcel/biobb_common
-      #     path: './biobb_common'
+      - name: Checkout biobb_common
+        uses: actions/checkout@v4
+        with:
+          repository: bioexcel/biobb_common
+          path: './biobb_common'
 
-      # - name: Run tests
-      #   shell: bash -l {0}
-      #   run: |
-      #     # Ignoring docker and singularity tests
-      #     export PYTHONPATH=.:./biobb_common:$PYTHONPATH
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          # Ignoring docker and singularity tests
+          export PYTHONPATH=.:./biobb_common:$PYTHONPATH
 
-      #     # Create directory for tests reports
-      #     mkdir -p ./reports/junit
+          # Create directory for tests reports
+          mkdir -p ./reports/junit
 
-      #     # Production one
-      #     pytest biobb_analysis/test/unitests/ --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.py
+          # Production one
+          pytest biobb_analysis/test/unitests/ --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.py
 
       # Notify user about test results
       - name: Comment on PR

diff --git a/biobb_analysis/gromacs/common.py b/biobb_analysis/gromacs/common.py
@@ -48,13 +48,11 @@ def check_energy_path(path, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_energy(file_extension[1:]):
         fu.log(
-            classname
-            + ": Format %s in energy input file is not compatible" % file_extension[1:],
+            classname + ": Format %s in energy input file is not compatible" % file_extension[1:],
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in energy input file is not compatible" % file_extension[1:]
+            classname + ": Format %s in energy input file is not compatible" % file_extension[1:]
         )
     # if file input has no path, add cwd because execution is launched on tmp folder
     if PurePath(path).name == path or not PurePath(path).is_absolute():
@@ -70,14 +68,12 @@ def check_input_path(path, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_structure(file_extension[1:]):
         fu.log(
-            classname
-            + ": Format %s in structure input file is not compatible"
+            classname + ": Format %s in structure input file is not compatible"
             % file_extension[1:],
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in structure input file is not compatible"
+            classname + ": Format %s in structure input file is not compatible"
             % file_extension[1:]
         )
     # if file input has no path, add cwd because execution is launched on tmp folder
@@ -93,13 +89,11 @@ def check_index_path(path, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_index(file_extension[1:]):
         fu.log(
-            classname
-            + ": Format %s in index input file is not compatible" % file_extension[1:],
+            classname + ": Format %s in index input file is not compatible" % file_extension[1:],
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in index input file is not compatible" % file_extension[1:]
+            classname + ": Format %s in index input file is not compatible" % file_extension[1:]
         )
     # if file input has no path, add cwd because execution is launched on tmp folder
     if PurePath(path).name == path or not PurePath(path).is_absolute():
@@ -115,14 +109,12 @@ def check_traj_path(path, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_trajectory(file_extension[1:]):
         fu.log(
-            classname
-            + ": Format %s in trajectory input file is not compatible"
+            classname + ": Format %s in trajectory input file is not compatible"
             % file_extension[1:],
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in trajectory input file is not compatible"
+            classname + ": Format %s in trajectory input file is not compatible"
             % file_extension[1:]
         )
     # if file input has no path, add cwd because execution is launched on tmp folder
@@ -139,13 +131,11 @@ def check_out_xvg_path(path, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_xvg(file_extension[1:]):
         fu.log(
-            classname
-            + ": Format %s in output file is not compatible" % file_extension[1:],
+            classname + ": Format %s in output file is not compatible" % file_extension[1:],
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in output file is not compatible" % file_extension[1:]
+            classname + ": Format %s in output file is not compatible" % file_extension[1:]
         )
     return path
 
@@ -158,13 +148,11 @@ def check_out_pdb_path(path, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_structure(file_extension[1:]):
         fu.log(
-            classname
-            + ": Format %s in output file is not compatible" % file_extension[1:],
+            classname + ": Format %s in output file is not compatible" % file_extension[1:],
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in output file is not compatible" % file_extension[1:]
+            classname + ": Format %s in output file is not compatible" % file_extension[1:]
         )
     return path
 
@@ -177,13 +165,11 @@ def check_out_traj_path(path, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_trajectory_output(file_extension[1:]):
         fu.log(
-            classname
-            + ": Format %s in output file is not compatible" % file_extension[1:],
+            classname + ": Format %s in output file is not compatible" % file_extension[1:],
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in output file is not compatible" % file_extension[1:]
+            classname + ": Format %s in output file is not compatible" % file_extension[1:]
         )
     return path
 
@@ -196,13 +182,11 @@ def check_out_str_ens_path(path, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_zip(file_extension[1:]):
         fu.log(
-            classname
-            + ": Format %s in output file is not compatible" % file_extension[1:],
+            classname + ": Format %s in output file is not compatible" % file_extension[1:],
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in output file is not compatible" % file_extension[1:]
+            classname + ": Format %s in output file is not compatible" % file_extension[1:]
         )
     return path