TODO: Fix bcpd

.github/env.yaml

@@ -4,5 +4,13 @@ channels:
   - bioconda
   - anaconda
 dependencies:
-  - biobb_common ==5.0.0
+  - biobb_common == 5.0.0
+  - numpy
+  - numpy-stl
+  - trimesh
+  - matplotlib
+  - scikit-learn
+  - scipy
+  - meshio
+  - rtree
 

.github/workflows/github-to-gitlab-push-sync.yml

@@ -18,6 +18,6 @@ jobs:
         fetch-depth: 0
     - uses: cniethammer/git-repo-sync@main
       with:
-        target-url: 'https://codehub.hlrs.de/coes/bioexcel/biobb/biobb_pytorch.git'
+        target-url: 'https://codehub.hlrs.de/coes/bioexcel/biobb/biobb_morph.git'
         target-username: ${{ secrets.ACCESS_TOKEN_NAME }}
         target-token: ${{ secrets.ACCESS_TOKEN }}

.github/workflows/linting_and_testing.yml

@@ -1,6 +1,6 @@
 name: tests
 
-on: 
+on:
   # workflow_dispatch
   push:
     branches: [ master ]
@@ -10,6 +10,8 @@ on:
       - 'LICENSE'
       - 'setup.py'
       - 'README.md'
+      - 'CITATION.cff'
+      - 'references.jsonld'
       - '**/docs/**'
       - '**/json_schemas/**'
 
@@ -19,17 +21,18 @@ jobs:
     strategy:
       matrix:
         os: [self-hosted]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
+        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 }}"
 
+
       - name: List files in the repository
         run: |
           ls ${{ github.workspace }}
@@ -39,11 +42,13 @@ jobs:
           rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null
           touch /home/user/.bash_profile
 
-      - name: provision-with-micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - name: setup-micromamba
+        uses: mamba-org/setup-micromamba@v2.0.0
         with:
           generate-run-shell: true
-          post-cleanup: all
+          micromamba-version: '2.0.2-2'
+          post-cleanup: 'all'
+          init-shell: bash
           environment-file: .github/env.yaml
           create-args: >-
             python=${{ matrix.python-version }}
@@ -52,60 +57,60 @@ jobs:
             pytest-html
             flake8
             pip
-      
+
       - name: Install genbadge from pip
-        shell: micromamba-shell {0}  # necessary for conda env to be active
+        shell: bash -l {0}
         run: pip install genbadge[all]
 
       - name: List installed package versions
-        shell: micromamba-shell {0}  # necessary for conda env to be active
+        shell: bash -l {0}
         run: micromamba list
 
       - name: Lint with flake8
-        shell: micromamba-shell {0}  # necessary for conda env to be active
+        shell: bash -l {0}
         run: |
           # F Codes: https://flake8.pycqa.org/en/latest/user/error-codes.html
           # E Code: https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
 
           # Workflow fails: Stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          
+
           # Create directory for flake8 reports
           mkdir -p ./reports/flake8
 
           # Exit-zero treats all errors as warnings, workflow will not fail:
-          flake8 . --exclude=docs --ignore=C901,E226,W605 --count --exit-zero --max-complexity=10 --max-line-length=9999 --statistics --format=html --htmldir=./reports/flake8/ --tee --output-file=./reports/flake8/flake8stats.txt
-      
+          flake8 . --exclude=docs --ignore=C901,E226 --count --exit-zero --max-complexity=10 --max-line-length=999 --statistics --format=html --htmldir=./reports/flake8/ --tee --output-file=./reports/flake8/flake8stats.txt
+
       - name: Generate Flake8 badge
-        shell: micromamba-shell {0}  # necessary for conda env to be active
+        shell: bash -l {0}
         run: |
           genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt  --output-file ./reports/flake8/flake8badge.svg
 
       - name: Checkout biobb_common
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: bioexcel/biobb_common
           path: './biobb_common'
 
       - name: Run tests
-        shell: micromamba-shell {0}  # necessary for conda env to be active
+        shell: bash -l {0}
         run: |
           # Ignoring docker and singularity tests
           export PYTHONPATH=.:./biobb_common:$PYTHONPATH
-          
+
           # Create directory for tests reports
           mkdir -p ./reports/junit
 
           # Producction one
-          pytest biobb_template/test/unitests/ --cov=biobb_template/ --cov-report=xml --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html
+          pytest biobb_morph/test/unitests/ --cov=biobb_morph/ --cov-report=xml --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.py --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html
 
       - name: Generate Tests badge
-        shell: micromamba-shell {0}  # necessary for conda env to be active
+        shell: bash -l {0}
         run: |
           genbadge tests --name "Tests" --input-file ./reports/junit/junit.xml  --output-file ./reports/junit/testsbadge.svg
 
       - name: Generate Coverage badge
-        shell: micromamba-shell {0}  # necessary for conda env to be active
+        shell: bash -l {0}
         run: |
           # Create directory for flake8 reports
           mkdir -p ./reports/coverage
@@ -118,6 +123,4 @@ jobs:
       - name: Publish coverage report to GitHub Pages
         uses: JamesIves/github-pages-deploy-action@v4
         with:
-          folder: ./reports
-
-
+          folder: ./reports

MANIFEST.in

@@ -0,0 +1 @@
+recursive-include biobb_morph/sources/ *

biobb_morph/__init__.py

@@ -1,3 +1,5 @@
+from . import morph
+
 name = "biobb_morph"
 __all__ = ["morph"]
-__version__ = "4.1.0"
+__version__ = "5.0.0"

biobb_morph/docs/source/change_log.md

@@ -1,30 +1,41 @@
 
 # Biobb Morph changelog
 
+## What's new in version [5.0.0](https://github.com/bioexcel/biobb_morph/releases/tag/v5.0.0)?
+
+### Changes
+
+* [CI/CD](linting_and_testing.yml): Update set-up micromamba.
+* [CI/CD](conf.yml): Adding global properties to test yaml configuration
+* [CI/CD](linting_and_testing.yaml): Update GA test workflow to Python >3.9
+* [DOCS](.readthedocs.yaml): Updating to Python 3.9
+* [CI/CD](GITIGNORE): Update .gitignore to include the new file extensions to ignore
+* [CI/CD](conf.yml): Change test conf.yml to adapt to new settings configuration
+
 ## What's new in version [4.1.0](https://github.com/bioexcel/biobb_morph/releases/tag/v4.1.0)?
-In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version. 
+In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version.
 
 ### New features
 
 * Update to biobb_common 4.1.0 (general)
 
 ## What's new in version [3.9.0](https://github.com/bioexcel/biobb_morph/releases/tag/v3.9.0)?
-In version 3.9.0 the dependency biobb_common has been updated to 3.9.0 version. 
+In version 3.9.0 the dependency biobb_common has been updated to 3.9.0 version.
 
 ### New features
 
 * Update to biobb_common 3.9.0 (general)
 * Version adapted to BioBB's notation (3.9.0)
 
 ## What's new in version [4.0.0](https://github.com/bioexcel/biobb_morph/releases/tag/v4.0.0)?
-In version 4.0.0 the dependency biobb_common has been updated to 3.8.1 version. 
+In version 4.0.0 the dependency biobb_common has been updated to 3.8.1 version.
 
 ### New features
 
 * Update to biobb_common 3.8.1 (general)
 
 ## What's new in version [3.0.0](https://github.com/bioexcel/biobb_morph/releases/tag/v3.0.0)?
-In version 3.0.0 the dependency biobb_common has been updated to 3.7.0 version. 
+In version 3.0.0 the dependency biobb_common has been updated to 3.7.0 version.
 
 ### New features