Merge pull request #129 from wilhelm-lab/release/0.5.0

Release/0.5.0
wilhelm-lab · Jul 11, 2024 · a34a547 · a34a547
2 parents 7b51ff1 + 8cb9098
commit a34a547
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Showing 36 changed files with 1,573 additions and 1,179 deletions.
diff --git a/.cookietemple.yml b/.cookietemple.yml
@@ -15,5 +15,5 @@ full_name: Mario Picciani
 email: mario.picciani@tum.de
 project_name: spectrum_io
 project_short_description: IO related functionalities for oktoberfest.
-version: 0.4.4
+version: 0.5.0
 license: MIT
diff --git a/.flake8 b/.flake8
@@ -6,6 +6,7 @@ max-complexity = 10
 docstring-convention = google
 per-file-ignores =
 	tests/*:S101,S301,S403
+    tests/unit_tests/test_parquet.py:B908,DAR101
 	noxfile.py:DAR101
 	spectrum_io/raw/thermo_raw.py:S603,S404
 	spectrum_io/raw/msraw.py:S405,S314

diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
@@ -1,5 +1,5 @@
-name-template: "0.4.4 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.4.4 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.5.0 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.5.0 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

diff --git a/.github/workflows/build_package.yml b/.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 }}
 

diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml
@@ -14,6 +14,6 @@ jobs:
               uses: actions/checkout@v4
 
             - name: Run Labeler
-              uses: crazy-max/ghaction-github-labeler@v4.1.0
+              uses: crazy-max/ghaction-github-labeler@v5.0.0
               with:
                   skip-delete: true
diff --git a/.github/workflows/main_master_branch_protection.yml b/.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

diff --git a/.github/workflows/publish_docs.yml b/.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: |

diff --git a/.github/workflows/publish_package.yml b/.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"
 

diff --git a/.github/workflows/run_cookietemple_lint.yml b/.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
 

diff --git a/.github/workflows/run_tests.yml b/.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 }}
 
@@ -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
@@ -136,10 +136,10 @@ jobs:
             - name: Check out the repository
               uses: actions/checkout@v4
 
-            - name: Set up Python 3.8
-              uses: actions/setup-python@v4
+            - name: Set up Python 3.9
+              uses: actions/setup-python@v5
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install Poetry
               run: |
@@ -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
 

diff --git a/.github/workflows/sync_project.yml b/.github/workflows/sync_project.yml
@@ -10,7 +10,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Setup Python
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: 3.8
 

diff --git a/cookietemple.cfg b/cookietemple.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.4
+current_version = 0.5.0
 
 [bumpversion_files_whitelisted]
 init_file = spectrum_io/__init__.py

diff --git a/docs/conf.py b/docs/conf.py
@@ -53,9 +53,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.4.4"
+version = "0.5.0"
 # The full version, including alpha/beta/rc tags.
-release = "0.4.4"
+release = "0.5.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/spectrum_io.file.rst b/docs/spectrum_io.file.rst
@@ -20,6 +20,14 @@ spectrum\_io.file.hdf5 module
    :undoc-members:
    :show-inheritance:
 
+spectrum\_io.file.parquet module
+-----------------------------
+
+.. automodule:: spectrum_io.file.parquet
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Module contents
 ---------------
 

diff --git a/noxfile.py b/noxfile.py
@@ -18,7 +18,7 @@
     sys.exit(1)
 
 package = "spectrum_io"
-python_versions = ["3.8", "3.9"]
+python_versions = ["3.9", "3.10"]
 nox.options.sessions = (
     "pre-commit",
     "safety",
@@ -125,9 +125,10 @@ def precommit(session: Session) -> None:
 @session(python=python_versions)
 def safety(session: Session) -> None:
     """Scan dependencies for insecure packages."""
+    to_ignore = "--ignore=70612"
     requirements = session.poetry.export_requirements()
     session.install("safety")
-    session.run("safety", "check", "--full-report", f"--file={requirements}")
+    session.run("safety", "check", "--full-report", f"--file={requirements}", to_ignore)
 
 
 @session(python=python_versions)