Add Parquet I/O

.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

.github/workflows/build_package.yml

@@ -9,7 +9,7 @@ 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

.github/workflows/publish_docs.yml

@@ -13,7 +13,7 @@ jobs:
             - name: Setup Python
               uses: actions/setup-python@v4
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install pip
               run: |

.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",
                       }
@@ -136,10 +136,10 @@ jobs:
             - name: Check out the repository
               uses: actions/checkout@v4
 
-            - name: Set up Python 3.8
+            - name: Set up Python 3.9
               uses: actions/setup-python@v4
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install Poetry
               run: |

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
 ---------------
 

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)

pyproject.toml

@@ -12,20 +12,20 @@ packages = [
     { include = "spectrum_io" },
 ]
 classifiers = [
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
 ]
 
 
 [tool.poetry.dependencies]
-python = ">=3.8.0,<3.11.0"
+python = ">=3.9.0,<3.11.0"
 click = ">=8.0.0"
 rich = ">=10.3.0"
 PyYAML = ">=5.4.1"
 numpy = "^1.18.1"
 pandas = "^1.3.0"
 h5py = "^3.1.0"
+pyarrow = ">=16.0.0"
 pymzml = "^2.5.0"
 pyteomics = "^4.3.3"
 lxml= '>=4.5.2,<6.0.0'
@@ -37,7 +37,7 @@ sortedcontainers = "^2.4.0"
 pytest = ">=6.2.3"
 coverage = {extras = ["toml"], version = ">=5.3"}
 safety = ">=1.9.0"
-typeguard = ">=2.12.0"
+typeguard = ">=3.0.0"
 xdoctest = {extras = ["colors"], version = ">=0.15.0"}
 sphinx = ">=4.0.2"
 sphinx-autobuild = ">=2021.3.14"

requirements.txt

@@ -1,42 +1,43 @@
-alphatims==1.0.8 ; python_version >= "3.8" and python_full_version < "3.11.0"
-click==8.1.7 ; python_version >= "3.8" and python_full_version < "3.11.0"
-colorama==0.4.6 ; python_version >= "3.8" and python_full_version < "3.11.0" and platform_system == "Windows"
-contourpy==1.1.1 ; python_version >= "3.8" and python_full_version < "3.11.0"
-cycler==0.12.1 ; python_version >= "3.8" and python_full_version < "3.11.0"
-fonttools==4.51.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-h5py==3.11.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.9"
-importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10"
-joblib==1.4.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-kiwisolver==1.4.5 ; python_version >= "3.8" and python_full_version < "3.11.0"
-llvmlite==0.41.1 ; python_version >= "3.8" and python_full_version < "3.11.0"
-lxml==4.9.4 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-markdown-it-py==3.0.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-matplotlib==3.7.5 ; python_version >= "3.8" and python_full_version < "3.11.0"
-mdurl==0.1.2 ; python_version >= "3.8" and python_full_version < "3.11.0"
-moepy==1.1.4 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-numba==0.58.1 ; python_version >= "3.8" and python_full_version < "3.11.0"
-numpy==1.24.4 ; python_version >= "3.8" and python_full_version < "3.11.0"
-packaging==24.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pandas==1.5.3 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pillow==10.3.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-psutil==5.9.8 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pygments==2.17.2 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-pymzml==2.5.9 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-pyparsing==3.1.2 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pyteomics==4.7.2 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pytz==2024.1 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pyyaml==6.0.1 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-pyzstd==0.15.10 ; python_version >= "3.8" and python_full_version < "3.11.0"
-regex==2024.4.16 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-rich==13.7.1 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-scikit-learn==1.3.2 ; python_version >= "3.8" and python_full_version < "3.11.0"
-scipy==1.10.1 ; python_version >= "3.8" and python_full_version < "3.11.0"
-six==1.16.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-sortedcontainers==2.4.0 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-spectrum-fundamentals==0.5.2 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-threadpoolctl==3.4.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-tqdm==4.66.2 ; python_version >= "3.8" and python_full_version < "3.11.0"
-typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.9"
-zipp==3.18.1 ; python_version >= "3.8" and python_version < "3.10"
+alphatims==1.0.8 ; python_version >= "3.9" and python_full_version < "3.11.0"
+click==8.1.7 ; python_version >= "3.9" and python_full_version < "3.11.0"
+colorama==0.4.6 ; python_version >= "3.9" and python_full_version < "3.11.0" and platform_system == "Windows"
+contourpy==1.1.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+cycler==0.12.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+fonttools==4.51.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+h5py==3.11.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+importlib-metadata==7.1.0 ; python_version >= "3.9" and python_version < "3.9"
+importlib-resources==6.4.0 ; python_version >= "3.9" and python_version < "3.10"
+joblib==1.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+kiwisolver==1.4.5 ; python_version >= "3.9" and python_full_version < "3.11.0"
+llvmlite==0.41.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+lxml==4.9.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+markdown-it-py==3.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+matplotlib==3.7.5 ; python_version >= "3.9" and python_full_version < "3.11.0"
+mdurl==0.1.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+moepy==1.1.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+numba==0.58.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+numpy==1.24.4 ; python_version >= "3.9" and python_full_version < "3.11.0"
+packaging==24.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pandas==1.5.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pillow==10.3.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+psutil==5.9.8 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pyarrow==16.1.0 ; python_full_version >= "3.9" and python_full_version < "3.11.0"
+pygments==2.17.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pymzml==2.5.9 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pyparsing==3.1.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pyteomics==4.7.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pytz==2024.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pyyaml==6.0.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pyzstd==0.15.10 ; python_version >= "3.9" and python_full_version < "3.11.0"
+regex==2024.4.16 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+rich==13.7.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+scikit-learn==1.3.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+scipy==1.10.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+six==1.16.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sortedcontainers==2.4.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+spectrum-fundamentals==0.5.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+threadpoolctl==3.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+tqdm==4.66.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+typing-extensions==4.11.0 ; python_version >= "3.9" and python_version < "3.9"
+zipp==3.18.1 ; python_version >= "3.9" and python_version < "3.10"

spectrum_io/file/__init__.py

@@ -2,6 +2,6 @@
 
 import logging
 
-from . import csv, hdf5
+from . import csv, hdf5, parquet
 
 logger = logging.getLogger(__name__)