Merge pull request #227 from wilhelm-lab/release/0.7.0

Release/0.7.0

.cookietemple.yml

@@ -15,5 +15,5 @@ full_name: Victor Giurcoiu
 email: [email protected]
 project_name: oktoberfest
 project_short_description: Public repo oktoberfest
-version: 0.6.2
+version: 0.7.0
 license: MIT

.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.6.2 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.6.2 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.7.0 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.7.0 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

.github/workflows/build_package.yml

@@ -9,14 +9,14 @@ jobs:
         strategy:
             matrix:
                 os: [macos-latest, ubuntu-latest, windows-latest]
-                python: [3.8, 3.9]
+                python: ["3.9", "3.10"]
 
         steps:
             - uses: actions/checkout@v4
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python }}
 

.github/workflows/main_master_branch_protection.yml

@@ -40,7 +40,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Set up Python
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: "3.8"
             # PRs to the repository master branch are only ok if coming from any patch or release branch

.github/workflows/publish_docs.yml

@@ -11,9 +11,9 @@ jobs:
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install pip
               run: |
@@ -30,7 +30,7 @@ jobs:
 
             - name: Deploy
               if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main'}}
-              uses: peaceiris/actions-gh-pages@v3
+              uses: peaceiris/actions-gh-pages@v4
               with:
                   github_token: ${{ secrets.GITHUB_TOKEN }}
                   publish_dir: ./docs/_build/html

.github/workflows/publish_package.yml

@@ -15,7 +15,7 @@ jobs:
                   fetch-depth: 2
 
             - name: Set up Python
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: "3.9"
 
@@ -29,7 +29,7 @@ jobs:
                   poetry build --ansi
 
             - name: Publish package on PyPI
-              uses: pypa/gh-action-pypi-publish@v1.8.10
+              uses: pypa/gh-action-pypi-publish@v1.9.0
               with:
                   user: __token__
                   password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/release_drafter.yml

@@ -14,6 +14,6 @@ jobs:
     update_release_draft:
         runs-on: ubuntu-latest
         steps:
-            - uses: release-drafter/release-drafter@v5
+            - uses: release-drafter/release-drafter@v6
               env:
                   GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/run_cookietemple_lint.yml

@@ -11,7 +11,7 @@ jobs:
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: 3.9
 

.github/workflows/run_tests.yml

@@ -19,47 +19,47 @@ jobs:
             matrix:
                 include:
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "pre-commit",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "safety",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "mypy",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: windows-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: macos-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "typeguard",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "xdoctest",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "docs-build",
                       }
@@ -72,7 +72,7 @@ jobs:
               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 }}
 
@@ -104,7 +104,7 @@ jobs:
                   print("::set-output name=result::{}".format(result))
 
             - name: Restore pre-commit cache
-              uses: actions/cache@v3.3.2
+              uses: actions/cache@v4.0.2
               if: matrix.session == 'pre-commit'
               with:
                   path: ~/.cache/pre-commit
@@ -116,15 +116,15 @@ jobs:
               run: nox --force-color --python=${{ matrix.python-version }}
 
             - name: Upload coverage data
-              if: always() && matrix.session == 'tests'
-              uses: actions/upload-artifact@v3
+              if: always() && matrix.session == 'tests' && matrix.os == 'ubuntu-latest'
+              uses: actions/upload-artifact@v4
               with:
                   name: coverage-data
                   path: ".coverage.*"
 
             - name: Upload documentation
               if: matrix.session == 'docs-build'
-              uses: actions/upload-artifact@v3
+              uses: actions/upload-artifact@v4
               with:
                   name: docs
                   path: docs/_build
@@ -137,7 +137,7 @@ jobs:
               uses: actions/checkout@v4
 
             - name: Set up Python 3.8
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: 3.8
 
@@ -154,7 +154,7 @@ jobs:
                   nox --version
 
             - name: Download coverage data
-              uses: actions/download-artifact@v3
+              uses: actions/download-artifact@v4
               with:
                   name: coverage-data
 
@@ -165,4 +165,4 @@ jobs:
               run: nox --force-color --session=coverage -- xml -i
 
             - name: Upload coverage report
-              uses: codecov/codecov-action@v3.1.4
+              uses: codecov/codecov-action@v4.5.0

.github/workflows/sync_project.yml

@@ -10,9 +10,9 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Setup Python
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install cookietemple
               run: pip install cookietemple

cookietemple.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.2
+current_version = 0.7.0
 
 [bumpversion_files_whitelisted]
 init_file = oktoberfest/__init__.py

docs/API.rst

@@ -62,23 +62,27 @@ Predicting: :code:`pr`
 
 .. currentmodule:: oktoberfest
 
-All things predictions
+Access to functions that communicate with a Koina server to retrieve predictions from various prediction models.
 
-Koina interface
-~~~~~~~~~~~~~~~
+High level features
+~~~~~~~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: api/pr
 
-   pr.predict
+   pr.predict_intensities
+   pr.predict_rt
+   pr.ce_calibration
 
-Postprocessing koina response
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Koina interface
+~~~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: api/pr
 
-   pr.parse_fragment_labels
+   pr.predict
+   pr.predict_at_once
+   pr.predict_in_chunks
 
 
 Rescoring: :code:`re`

docs/_key_contributors.rst

@@ -1,14 +1,25 @@
 .. sidebar:: Key Contributors
 
-   * `Mario Picciani <https://github.com/picciama>`_: developer, maintainer
-   * `Wassim Gabriel <https://github.com/WassimG>`_: developer, maintainer
-   * `Matthew The <https://github.com/MatthewThe>`_: developer, maintainer
-   * `Ludwig Lautenbacher <https://github.com/LLautenbacher>`_: developer, maintainer
-   * `Victor-George Giurcoiu <https://github.com/victorgiurcoiu>`_: developer
-   * `Omar Shouman <https://github.com/omsh>`_: developer
-   * Firas Hamood: developer
-   * Cecilia Jensen: developer
-   * Julian Mueller: developer
-   * `Mostafa Kalhor <https://github.com/mostafakalhor>`_: developer
-   * `Armin Soleymaniniya <https://github.com/arminsl>`_: developer
+   Current developers
+
+   * `Mario Picciani <https://github.com/picciama>`_: lead developer since 2022, maintainer
+   * `Mostafa Kalhor <https://github.com/mostafakalhor>`_: developer, crosslinking
+   * `Wassim Gabriel <https://github.com/WassimG>`_: developer, PTMs, neutral losses, GUI
+   * Arne van den Berg: developer, diverse contributions
+   * `Victor-George Giurcoiu <https://github.com/victorgiurcoiu>`_: developer, diverse contributions
+   * `Ludwig Lautenbacher <https://github.com/LLautenbacher>`_: developer, Koina, GUI
+   * `Armin Soleymaniniya <https://github.com/arminsl>`_: developer, GUI
+   * Ayla Schröder: developer, pickedGroupFDR
+   * Zixuan Xiao: developer, GUI
+
+   Previous developers
+
+   * `Matthew The <https://github.com/MatthewThe>`_: developer, percolator
+   * `Omar Shouman <https://github.com/omsh>`_: developer, diverse contributions
+   * Firas Hamood: developer, diverse contributions
+   * Cecilia Jensen: developer, diverse contributions
+   * Julian Mueller: developer, diverse contributions
+
+   Other roles
+
    * `Mathias Wilhelm <https://github.com/mwilhelm42>`_: advisor and PI of wilhelmlab

docs/_static/custom_cookietemple.css

@@ -48,6 +48,10 @@ table.align-default {
     padding-left: 50px;
 }
 
+.main-config-table tbody tr:nth-child(n + 7):nth-child(-n + 7) td:nth-child(1) {
+    padding-left: 50px;
+}
+
 .lib-rescore-config-table
     tbody
     tr:nth-child(n + 2):nth-child(-n + 5)
@@ -63,7 +67,7 @@ table.align-default {
     padding-left: 50px;
 }
 
-.lib-config-table tbody tr:nth-last-child(-n + 6) td:nth-child(1) {
+.lib-config-table tbody tr:nth-last-child(-n + 7) td:nth-child(1) {
     padding-left: 50px;
 }
 

docs/conf.py

@@ -54,9 +54,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.6.2"
+version = "0.7.0"
 # The full version, including alpha/beta/rc tags.
-release = "0.6.2"
+release = "0.7.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -195,6 +195,7 @@
     scipy=("https://docs.scipy.org/doc/scipy/", None),
     seaborn=("https://seaborn.pydata.org/", None),
     sklearn=("https://scikit-learn.org/stable/", None),
+    anndata=("https://anndata.readthedocs.io/en/stable", None),
 )