Use pyproject toml instead of setup.py (#382)

.readthedocs.yml

@@ -7,9 +7,10 @@ build:
 
 python:
   install:
-    - requirements: requirements-rtd.txt
     - method: pip
       path: .
+      extra_requirements:
+        - docs
 
 sphinx:
   configuration: docs/source/conf.py

CHANGELOG.md

@@ -4,6 +4,9 @@
 
 ### Fixes
 
+## Improvements
+* Use `pyproject.toml` for project metadata and installation requirements [#382](https://github.com/catalystneuro/roiextractors/pull/382)
+
 
 # v0.5.10 (November 6th, 2024)
 

docs/source/gettingstarted.rst

@@ -9,17 +9,23 @@ Installation
 
        $ pip install roiextractors
 
-#. You can check for any missing packages by explicitly installing from the `requirements <https://github.com/catalystneuro/roiextractors/blob/master/requirements.txt/>`_ file:
-    .. code-block:: shell
-
-        $ pip install -r requirements.txt
 
 #. **Cloning the github repo**:
     .. code-block:: shell
 
         $ git clone https://github.com/SpikeInterface/spikeinterface.git
         $ cd spikeinterface
-        $ python setup.py install (or develop)
+        $ pip install --editable .
+
+You can also install the optional dependencies by installing the package with the following command:
+
+.. code-block:: shell
+
+    $ pip install "roiextractors[full]"
+    $ pip install "roiextractors[test]"
+    $ pip install "roiextractors[docs]"
+
+These commands install the full, test, and documentation dependencies, respectively.
 
 What is RoiExtractors
 ---------------------

pyproject.toml

@@ -1,3 +1,84 @@
+[build-system]
+requires = ["setuptools>=64"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "roiextractors"
+version = "0.5.11"
+description = "Python module for extracting optical physiology ROIs and traces for various file types and formats"
+readme = "README.md"
+license = { file = "LICENSE.txt" }
+authors = [
+    { name = "Heberto Mayorquin" },
+    { name = "Szonja Weigl" },
+    { name = "Cody Baker" },
+    { name = "Ben Dichter", email = "[email protected]" },
+    { name = "Alessio Buccino" },
+    { name = "Paul Adkisson" },
+    { name = "Alessandra Trapani" }
+]
+keywords = ["ROI", "extraction", "optical physiology"]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: MacOS",
+    "License :: OSI Approved :: BSD License",
+]
+requires-python = ">=3.9"
+
+dependencies = [
+  "h5py>=2.10.0",
+  "pynwb>=2.0.1",
+  "tqdm>=4.48.2",
+  "lazy_ops>=0.2.0",
+  "dill>=0.3.2",
+  "scipy>=1.5.2",
+  "psutil>=5.8.0",
+  "PyYAML",
+  "lxml",
+  "packaging"
+]
+
+[project.optional-dependencies]
+full = [
+    "tifffile>=2018.10.18",
+    "scanimage-tiff-reader>=1.4.1.4",
+    "neuroconv[video]>=0.4.6",
+    "opencv-python-headless>=4.8.1.78",
+    "natsort>=8.3.1",
+    "isx>=1.0.4"
+]
+test = [
+    "pytest",
+    "pytest-cov",
+    "parameterized==0.8.1",
+    "spikeinterface>=0.100.7",
+    "pytest-xdist"
+]
+docs = [
+    "Jinja2",
+    "Sphinx",
+    "sphinx_rtd_theme",
+    "readthedocs-sphinx-search",
+    "sphinx-toggleprompt",
+    "sphinx-copybutton",
+    "pydata_sphinx_theme"
+]
+
+[project.urls]
+"Homepage" = "https://github.com/catalystneuro/roiextractors"
+"Documentation" = "https://roiextractors.readthedocs.io//"
+"Changelog" = "https://github.com/catalystneuro/roiextractors/blob/main/CHANGELOG.md"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+
 
 [tool.black]
 line-length = 120

tests/setup_paths.py

@@ -1,31 +1,43 @@
 import os
-import json
+import tempfile
 from pathlib import Path
-from tempfile import mkdtemp
+from shutil import copy
+import json
 
-import pytest
+# Output by default to a temporary directory
+OUTPUT_PATH = Path(tempfile.mkdtemp())
 
 
-file_path = Path(__file__).parent / "gin_test_config.json"
+# Load the configuration for the data tests
 
-with open(file=file_path) as f:
-    test_config_dict = json.load(f)
 
 if os.getenv("CI"):
     LOCAL_PATH = Path(".")  # Must be set to "." for CI
     print("Running GIN tests on Github CI!")
 else:
     # Override LOCAL_PATH in the `gin_test_config.json` file to a point on your system that contains the dataset folder
     # Use DANDIHub at hub.dandiarchive.org for open, free use of data found in the /shared/catalystneuro/ directory
+    test_config_path = Path(__file__).parent / "gin_test_config.json"
+    config_file_exists = test_config_path.exists()
+    if not config_file_exists:
+
+        root = test_config_path.parent.parent
+        base_test_config_path = root / "base_gin_test_config.json"
+
+        test_config_path.parent.mkdir(parents=True, exist_ok=True)
+        copy(src=base_test_config_path, dst=test_config_path)
+
+    with open(file=test_config_path) as f:
+        # Load the configuration for the data tests
+        test_config_dict = json.load(f)
+
     LOCAL_PATH = Path(test_config_dict["LOCAL_PATH"])
-    print("Running GIN tests locally!")
+
+    if test_config_dict["SAVE_OUTPUTS"]:
+        OUTPUT_PATH = LOCAL_PATH / "neuroconv_test_outputs"
+        OUTPUT_PATH.mkdir(exist_ok=True, parents=True)
+
 
 OPHYS_DATA_PATH = LOCAL_PATH / "ophys_testing_data"
-if not OPHYS_DATA_PATH.exists():
-    pytest.fail(f"No folder found in location: {OPHYS_DATA_PATH}!")
 
-if test_config_dict["SAVE_OUTPUTS"]:
-    OUTPUT_PATH = LOCAL_PATH / "example_nwb_output"
-    OUTPUT_PATH.mkdir(exist_ok=True)
-else:
-    OUTPUT_PATH = Path(mkdtemp())
+TEXT_DATA_PATH = Path(__file__).parent.parent.parent / "tests" / "test_text"