Remove pytables as a dependency

.github/workflows/pip_installation.yml

@@ -22,16 +22,15 @@ jobs:
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
-      install-script: pip_install.sh stable,tests alphabase ${{ matrix.python-version }} ${{ matrix.os }}
+      install-script: pip_install.sh stable,tests
 
   loose_installation:
     name: Test loose pip installation on ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
-        python-version: [3.9]
     uses: ./.github/workflows/_run_tests.yml
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
-      install-script: pip_install.sh tests alphabase ${{ matrix.python-version }} ${{ matrix.os }}
+      install-script: pip_install.sh tests

README.md

@@ -97,25 +97,11 @@ be compatible with:
 pip install "alphabase[stable]"
 ```
 
-**NOTE**: You might need to run `pip install -U pip` before installing
+NOTE: You might need to run `pip install -U pip` before installing
 AlphaBase like this. Also note the double quotes `"`.
 If you are using the `quant_reader` module, it is advisable to add the
-`dask-stable` or `dask` extras to speed up processing large files.
-
-**NOTE for macOS users**: Due to compilation issues with PyTables on macOS, you may encounter build errors when installing AlphaBase.
-These may include
-
-- `ERROR:: Could not find a local HDF5 installation`
-- `ERROR: Failed building wheel for tables`
-
-If this happens, install PyTables via conda/mamba first:
-```bash
-conda install -c conda-forge pytables
-# or
-mamba install -c conda-forge pytables
-```
-Then proceed with the pip installation of AlphaBase.
-
+`dask-stable` or `dask` extras to speed up processing large files. You need to install the `hdf` option
+of the package to be able to read alphapept protein group matrices in hdf format.
 
 For those who are really adventurous, it is also possible to directly
 install any branch (e.g. `@main`) with any extras

alphabase/pg_reader/alphapept_pg_reader.py

@@ -22,6 +22,9 @@ class AlphaPeptPGReader(PGReaderBase):
     AlphaPept protein group matrices contain both raw intensities and LFQ-corrected intensities.
     The LFQ-corrected intensities are marked by an `_LFQ` suffix.
 
+    In order to read alphapept `.hdf` output, please install the package with extra optional
+    dependencies `pip install alphabase[hdf]`.
+
     Example:
     -------
     Get example data

misc/pip_install.sh

@@ -8,7 +8,6 @@ set -e -u
 INSTALL_TYPE=$1 # stable, loose, etc..
 ENV_NAME=${2:-alphabase}
 PYTHON_VERSION=${3:-3.9}
-OS=${4:-nan}
 
 conda create -n $ENV_NAME python=$PYTHON_VERSION -y
 
@@ -18,12 +17,6 @@ else
   INSTALL_STRING="[${INSTALL_TYPE}]"
 fi
 
-# pytables has known issues on MacOS for pg-readers - install from conda
-# https://github.com/PyTables/PyTables/issues/219#issuecomment-24117053
-if [[ "$OS" = "macOS-latest" || "$OS" = "macos-latest-xlarge" ]]; then
-  conda install -n $ENV_NAME -c conda-forge pytables -y
-fi
-
 # print pip environment for reproducibility
 conda run -n $ENV_NAME --no-capture-output pip freeze
 

pyproject.toml

@@ -51,6 +51,7 @@ dependencies = {file = ["requirements/requirements_loose.txt"]}
 optional-dependencies.stable = { file = ["requirements/requirements.txt" ] }
 optional-dependencies.dask = { file = ["requirements/requirements_dask_loose.txt" ] }
 optional-dependencies.dask-stable = { file = ["requirements/requirements_dask.txt" ] }
+optional-dependencies.hdf = { file = ["requirements/requirements_hdf_loose.txt" ] }
 optional-dependencies.tests = { file = ["requirements/requirements_tests.txt" ] }
 optional-dependencies.development = { file = [
     "requirements/requirements_development.txt",

requirements/requirements.txt

@@ -17,4 +17,3 @@ pyteomics==4.7.5
 pyyaml==6.0.2
 lxml==5.3.0  # required by pyteomics
 rdkit==2024.3.3
-tables==3.9.2 # required to read HDF files, latest version compatible with 3.9

requirements/requirements_hdf_loose.txt

@@ -0,0 +1,2 @@
+# Dependencies required for running the "loose" version of alphabase with hdf support for the alphapept PG reader.
+tables

requirements/requirements_loose.txt

@@ -15,4 +15,3 @@ pyteomics
 pyyaml
 lxml
 rdkit
-tables

tests/integration/conftest.py

@@ -1,5 +1,6 @@
 """Shared logic for integration tests."""
 
+import importlib.util
 import os
 from pathlib import Path
 
@@ -8,6 +9,14 @@
 
 from alphabase.tools.data_downloader import DataShareDownloader
 
+TABLES_PACKAGE_UNAVAILABLE = importlib.util.find_spec("tables") is None
+
+
+pytest.mark.optional_pytables_dependency = pytest.mark.skipif(
+    TABLES_PACKAGE_UNAVAILABLE,
+    reason="pytables package not installed. Install with `pip install alphabase[hdf]`",
+)
+
 
 def get_remote_data_with_ref(
     url: str, ref_url: str, directory: Path
@@ -132,6 +141,7 @@ def example_alphapept_csv(tmp_path) -> tuple[Path, pd.DataFrame]:
     return file_path, reference
 
 
+@pytest.mark.optional_pytables_dependency
 @pytest.fixture(scope="function")
 def example_alphapept_hdf(tmp_path) -> tuple[Path, pd.DataFrame]:
     """Get and parse real alphapept protein group report matrix."""

tests/integration/test_pg_readers.py

@@ -51,6 +51,7 @@ def test_import_csv_file_equivalent(
 
         pd.testing.assert_frame_equal(result_df, reference)
 
+    @pytest.mark.optional_pytables_dependency
     def test_import_hdf_file_equivalent(
         self, example_alphapept_hdf: tuple[str, pd.DataFrame]
     ):
@@ -105,6 +106,7 @@ def test_import_csv_file(
             PGCols.DECOY_INDICATOR,
         ]
 
+    @pytest.mark.optional_pytables_dependency
     @pytest.mark.parametrize(
         ("measurement_regex", "expected_shape", "expected_colums"),
         [