Compatability updates

.github/workflows/CI_build.yml

@@ -8,39 +8,39 @@ on:
 jobs:
 
   first_check:
-    name: first code check / python-3.8 / ubuntu-latest
+    name: first code check / python-3.10 / ubuntu-latest
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: "3.10"
       - name: Python info
         run: |
           which python
           python --version
       - name: Build package and create dev environment
         run: |
-          python -m pip install --upgrade pip
-          pip install -e .[dev]
+          python -m pip install --upgrade pip poetry
+          poetry install
       - name: Show pip list
         run: |
           pip list
       - name: Test with coverage
         run: |
-          pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
+          poetry run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
       - name: Correct coverage paths
         run: sed -i "s+$PWD/++g" coverage.xml
       - name: Check style against standards using prospector
         shell: bash -l {0}
-        run: prospector -o grouped -o pylint:pylint-report.txt
+        run: poetry run prospector -o grouped -o pylint:pylint-report.txt
       - name: Check whether import statements are used consistently
         shell: bash -l {0}
-        run: isort --check-only --diff --conda-env spec2vec-dev .
-      - name: SonarCloud Scan
+        run: poetry run isort --check-only --diff --conda-env spec2vec-dev .
+      - name: SonarQube Scan
         if: github.repository == 'iomega/spec2vec'
-        uses: sonarsource/sonarcloud-github-action@master
+        uses: SonarSource/sonarqube-scan-action@master
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
@@ -53,15 +53,15 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.10']
         exclude:
           # already tested in first_check job
-          - python-version: 3.8
+          - python-version: "3.10"
             os: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Python info
@@ -70,31 +70,31 @@ jobs:
           python --version
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
+          python -m pip install --upgrade pip poetry
       - name: Build package
         run: |
-          pip install wheel twine
-          python setup.py sdist bdist_wheel
+          poetry build
       - name: Test package
         run: |
+          pip install twine
           python -m twine check dist/*
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip poetry
+          poetry install
       - name: Show pip list
         run: |
           pip list
-      - name: Install development dependencies
-        run: |
-          pip install -e .[dev]
       - name: Test
         run: |
-          pytest
+          poetry run pytest
       - name: Show environment variables
         shell: bash -l {0}
         run: |
           env | sort
       - name: Build documentation
-        shell: bash -l {0}
         run: |
-          make coverage doctest html
+          poetry run make coverage doctest html
         working-directory: readthedocs/
         env:
           SPHINXOPTS: "-n"  # enable nit-picky mode
@@ -108,22 +108,22 @@ jobs:
           echo "The code is sufficiently documented with ${UNCOVERED_MEMBERS} uncovered members out of ${UNCOVERED_MEMBERS_ALLOWED} allowed.";
 
   anaconda_build:
-    name: Anaconda build / python-3.7 / ubuntu-latest
+    name: Anaconda build / python-3.10 / ubuntu-latest
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
     needs: first_check
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: "0"
       - name: Create spec2vec-build environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: spec2vec-build
           auto-update-conda: true
           environment-file: conda/environment-build.yml
-          python-version: 3.8
+          python-version: "3.10"
       - name: Show conda config
         shell: bash -l {0}
         run: |
@@ -148,11 +148,11 @@ jobs:
           [ "$RUNNING_OS" = "Windows" ] && export BUILDDIR=$RUNNER_TEMP\\spec2vec\\_build\\
           conda config --set anaconda_upload no
           conda build --no-include-recipe \
-            --channel bioconda --channel conda-forge \
+            --channel conda-forge --channel bioconda \
             --croot ${BUILDDIR} \
             ./conda
       - name: Upload package artifact from build
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: conda-package-artifact
           path: ${{ runner.temp }}/spec2vec/_build

.github/workflows/cffconvert.yml

@@ -0,0 +1,19 @@
+name: cffconvert
+
+on:
+  push:
+    paths:
+      - CITATION.cff
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@v2
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/[email protected]
+        with:
+          args: "--validate"

.github/workflows/pypi_publish.yml

@@ -5,21 +5,11 @@ on:
     types: [published]
 
 jobs:
-  publish:
+  build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v1
-      with:
-        python-version: 3.7
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-        python setup.py sdist bdist_wheel
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_TOKEN }}
+      - uses: actions/checkout@v4
+      - name: Build and publish to pypi
+        uses: JRubics/[email protected]
+        with:
+          pypi_token: ${{ secrets.PYPI_TOKEN }}

.gitignore

@@ -16,8 +16,8 @@ pylint-report.txt
 xunit-result.xml
 .scannerwork/
 
-docs/_build
-docs/apidocs
+readthedocs/_build
+readthedocs/api
 
 # ide
 .idea

CHANGELOG.md

@@ -7,6 +7,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.9.0] - 2025-10-20
+### Changed
+- Added loss_mz_from and loss_mz_to to SpectrumDocument [#95](https://github.com/iomega/spec2vec/pull/95)
+- Updated required matchms version to >=0.27.0 [#95](https://github.com/iomega/spec2vec/pull/95)
+- Updated required Python version to >=3.10 [#95](https://github.com/iomega/spec2vec/pull/95)
+- Moved to poetry [#95](https://github.com/iomega/spec2vec/pull/95)
+- Updated CI_build workflow to use poetry and actions [#95](https://github.com/iomega/spec2vec/pull/95)
+- Added sparse array type handling and tests [#95](https://github.com/iomega/spec2vec/pull/95)
+
+### Fixed
+
+- Fixed missing keyword in model dict [#95](https://github.com/iomega/spec2vec/pull/95)
+- Fixed documentation [#95](https://github.com/iomega/spec2vec/pull/95)
+
 ## [0.8.1] - 2024-08-06
 ### Changed
 - Set max matchms to 0.26.4
@@ -147,7 +161,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fossa configuration
 - Flowchart
 
-[Unreleased]: https://github.com/iomega/spec2vec/compare/0.8.0...HEAD
+[Unreleased]: https://github.com/iomega/spec2vec/compare/0.9.0...HEAD
+[0.9.0]: https://github.com/iomega/spec2vec/compare/0.8.1...0.9.0
+[0.8.1]: https://github.com/iomega/spec2vec/compare/0.8.0...0.8.1
 [0.8.0]: https://github.com/iomega/spec2vec/compare/0.6.0...0.7.0
 [0.7.0]: https://github.com/iomega/spec2vec/compare/0.6.0...0.7.0
 [0.6.0]: https://github.com/iomega/spec2vec/compare/0.5.0...0.6.0

CITATION.cff

@@ -64,7 +64,7 @@ authors:
     given-names: Maksym
     orcid: "https://orcid.org/0000-0003-2056-8018"
 
-cff-version: "1.1.0"
+cff-version: 1.2.0
 keywords:
   - Word2Vec
   - "similarity measures"

README.rst

@@ -66,7 +66,6 @@ Thanks!
 
 .. |ReadTheDocs Badge| image:: https://readthedocs.org/projects/spec2vec/badge/?version=latest
     :alt: Documentation Status
-    :scale: 100%
     :target: https://spec2vec.readthedocs.io/en/latest/?badge=latest
 
 .. |Sonarcloud Quality Gate Badge| image:: https://sonarcloud.io/api/project_badges/measure?project=iomega_spec2vec&metric=alert_status
@@ -139,7 +138,6 @@ dataset.
         s = msfilters.normalize_intensities(s)
         s = msfilters.reduce_to_number_of_peaks(s, n_required=10, ratio_desired=0.5, n_max=500)
         s = msfilters.select_by_mz(s, mz_from=0, mz_to=1000)
-        s = msfilters.add_losses(s, loss_mz_from=10.0, loss_mz_to=200.0)
         s = msfilters.require_minimum_number_of_peaks(s, n_required=10)
         return s
 
@@ -150,7 +148,7 @@ dataset.
     spectrums = [s for s in spectrums if s is not None]
 
     # Create spectrum documents
-    reference_documents = [SpectrumDocument(s, n_decimals=2) for s in spectrums]
+    reference_documents = [SpectrumDocument(s, n_decimals=2, loss_mz_from=10.0, loss_mz_to=200.0) for s in spectrums]
 
     model_file = "references.model"
     model = train_new_word2vec_model(reference_documents, iterations=[10, 20, 30], filename=model_file,

conda/environment-build.yml

@@ -5,4 +5,4 @@ dependencies:
   - anaconda-client
   - conda-build
   - conda-verify
-  - python >=3.7
+  - python >=3.10

conda/environment-dev.yml

@@ -3,15 +3,23 @@ channels:
   - bioconda
   - conda-forge
   - defaults
-  - nlesc
 dependencies:
-  - gensim >=4.2.0
-  - matchms >=0.6.2
-  - numba >=0.51
+  - python
+  - gensim >=4.4.0
+  - matchms >=0.27.0
+  - numba
   - numpy
   - pip
-  - python >=3.7
   - scipy
   - tqdm
-  - pip:
-    - -e ..[dev]
+  - bump2version
+  - isort>=5.1.0
+  - pylint<2.12.0
+  - prospector
+  - pytest
+  - pytest-cov
+  - sphinx>=4.0.0
+  - sphinx_rtd_theme
+  - sphinxcontrib-apidoc
+  - yapf
+