Merge pull request #2770 from galenlynch/packaging/pyproject.toml

Migrate from setup.py to pyproject.toml (hatchling)

Author: mikejhuang

.github/workflows/github-actions-ci.yml

@@ -57,13 +57,10 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
-          cache-dependency-path: |
-            requirements.txt
-            test_requirements.txt
+          cache-dependency-path: pyproject.toml
       - name: Install
         run: |
-          pip install -r test_requirements.txt
-          pip install .
+          pip install -e ".[test]"
       - name: Test
         run: |
           python -m pytest -n 4 ${{ (matrix.os == 'ubuntu-latest' && matrix.python-version == '3.13') && '--cov=allensdk' || '' }}
@@ -86,8 +83,7 @@ jobs:
               --mount type=tmpfs,destination=/tmp \
               --rm \
               ${{ matrix.image }} \
-                  /bin/bash -c "pip install -r requirements.txt; \
-                                pip install -r test_requirements.txt; \
+                  /bin/bash -c "pip install -e '.[test]'; \
                                 python -m pytest \
                                     --log-level=INFO \
                                     --capture=no \

.github/workflows/nightly.yml

@@ -26,9 +26,7 @@ jobs:
               --mount type=tmpfs,destination=/tmp \
               --rm \
               ${{ matrix.image }} \
-                  /bin/bash -c "pip install -r requirements.txt; \
-                                pip install -r test_requirements.txt; \
-                                pip install -e .; \
+                  /bin/bash -c "pip install -e '.[test]'; \
                                 python -m pytest \
                                     --log-level=INFO \
                                     --capture=no \

.github/workflows/notebook_runner.yml

@@ -18,16 +18,10 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
-          cache-dependency-path: |
-            requirements.txt
-            dev_requirements.txt
-            notebook_requirements.txt
+          cache-dependency-path: pyproject.toml
       - name: Install
         run: |
-          pip install -r requirements.txt
-          pip install -r dev_requirements.txt
-          pip install -r notebook_requirements.txt
-          pip install .
+          pip install -e ".[dev,notebooks]"
           ipython kernel install --name "python3" --user
       - name: Run notebooks
         run: |

.gitignore

@@ -32,4 +32,4 @@ debug.log
 /cell_types/
 example_ecephys_project_cache/
 .DS_Store
-/venv/
+/venv/

.readthedocs.yml

@@ -10,11 +10,13 @@ sphinx:
 build:
   os: ubuntu-22.04
   tools:
-      python: "3.8"
-
+      python: "3.13"
 python:
    install:
-      - requirements: doc_requirements.txt
+      - method: pip
+        path: .
+        extra_requirements:
+          - docs
 
 formats:
   - epub

CONTRIBUTING.md

@@ -36,7 +36,7 @@ If you are comfortable addressing this issue yourself, take a look at the [guide
 Adding example notebooks are a great way to contribute to documentation and help
 other users get started on the AllenSDK. Take a look at our [existing notebooks](https://github.com/AllenInstitute/AllenSDK/tree/master/doc_template/examples_root/examples/nb)
 as a general guide for the style and content. We have many great notebooks, but 
-[Extracellular Electrophysiology Data](https://github.com/AllenInstitute/AllenSDK/blob/master/doc_template/examples_root/examples/nb/ecephys_session.ipynb) is a good one to take a look at to get a sense for what we're looking for. All new notebook contributions should be compatible with Python 3.6+.
+[Extracellular Electrophysiology Data](https://github.com/AllenInstitute/AllenSDK/blob/master/doc_template/examples_root/examples/nb/ecephys_session.ipynb) is a good one to take a look at to get a sense for what we're looking for. All new notebook contributions should be compatible with Python 3.10+.
 
 Notebook Guidelines:
 
@@ -112,14 +112,14 @@ visual git plugins, we prefer the following convention for branch naming:
     GH-712/bugfix/auto-reward-key
     GH-9999/feature/parallel-behavior-analysis
     ```
-* Create an environment and install necessary requirements: `requirements.txt` and `test_requirements.txt`
+* Create an environment and install with test dependencies: `pip install -e ".[test]"`
 * Start writing code!
 
 ### Style Guidelines
 We follow [PEP-8 guidelines](https://www.python.org/dev/peps/pep-0008/) for new python code.
 We also follow [PEP-484](https://www.python.org/dev/peps/pep-0484/) for type annotations.
 Before submitting a pull request, run [flake8](https://pypi.python.org/pypi/flake8/) and 
-[mypy](https://pypi.org/project/mypy/) linters to check the style of your code. All new code contributions should be compatible with Python 3.6+.
+[mypy](https://pypi.org/project/mypy/) linters to check the style of your code. All new code contributions should be compatible with Python 3.10+.
 
 #### Docstrings
 Docstrings for new code should follow the [Numpy docstring standard](https://numpydoc.readthedocs.io/en/latest/format.html). This allows us to ensure consistency in our auto-generated API documentation.

MANIFEST.in

@@ -34,16 +34,12 @@
 # POSSIBILITY OF SUCH DAMAGE.
 #
 import logging
-
-__version__ = '2.16.2'
-
+from importlib.metadata import version, PackageNotFoundError
 
 try:
-    from logging import NullHandler
-except ImportError:
-    class NullHandler(logging.Handler):
-        def emit(self, record):
-            pass
+    __version__ = version("allensdk")
+except PackageNotFoundError:
+    __version__ = "0.0.0.dev0"
 
 
 class OneResultExpectedError(RuntimeError):
@@ -66,7 +62,7 @@ def one(x):
         return x[0]
 
 
-logging.getLogger(__name__).addHandler(NullHandler())
+logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 if True:
     file_download_log = logging.getLogger(

allensdk/__init__.py

@@ -38,12 +38,8 @@
 import os
 import logging
 import logging.config as lc
-from pkg_resources import resource_filename  # @UnresolvedImport
-
-try:
-    from configparser import ConfigParser  # @UnresolvedImport
-except:
-    from ConfigParser import ConfigParser  # @UnresolvedImport
+from configparser import ConfigParser
+from importlib.resources import files
 
 
 class ApplicationConfig(object):
@@ -54,7 +50,7 @@ class ApplicationConfig(object):
 
     _log = logging.getLogger(__name__)
     _DEFAULT_LOG_CONFIG = os.getenv(
-        'LOG_CFG', resource_filename(__name__, 'logging.conf'))
+        'LOG_CFG', str(files(__package__).joinpath('logging.conf')))
 
     def __init__(self,
                  defaults,

allensdk/config/app/application_config.py

@@ -40,7 +40,7 @@
 import six
 import itertools
 import logging
-from pkg_resources import parse_version
+from packaging.version import Version
 
 import h5py
 import pandas as pd
@@ -145,9 +145,9 @@ def __init__(self, nwb_file):
             meta = self.get_metadata()
             if meta and 'pipeline_version' in meta:
                 pipeline_version_str = meta['pipeline_version']
-                self.pipeline_version = parse_version(pipeline_version_str)
+                self.pipeline_version = Version(pipeline_version_str)
 
-                if self.pipeline_version > parse_version(self.SUPPORTED_PIPELINE_VERSION):
+                if self.pipeline_version > Version(self.SUPPORTED_PIPELINE_VERSION):
                     logging.warning("File %s has a pipeline version newer than the version supported by this class (%s vs %s)."
                                     " Please update your AllenSDK." % (nwb_file, pipeline_version_str, self.SUPPORTED_PIPELINE_VERSION))
 
@@ -289,7 +289,7 @@ def get_neuropil_traces(self, cell_specimen_ids=None):
         timestamps = self.get_fluorescence_timestamps()
 
         with h5py.File(self.nwb_file, 'r') as f:
-            if self.pipeline_version >= parse_version("2.0"):
+            if self.pipeline_version >= Version("2.0"):
                 ds = f['processing'][self.PIPELINE_DATASET][
                     'Fluorescence']['imaging_plane_1_neuropil_response']['data']
             else:
@@ -321,7 +321,7 @@ def get_neuropil_r(self, cell_specimen_ids=None):
         '''
 
         with h5py.File(self.nwb_file, 'r') as f:
-            if self.pipeline_version >= parse_version("2.0"):
+            if self.pipeline_version >= Version("2.0"):
                 r_ds = f['processing'][self.PIPELINE_DATASET][
                     'Fluorescence']['imaging_plane_1_neuropil_response']['r']
             else:
@@ -388,7 +388,7 @@ def get_corrected_fluorescence_traces(self, cell_specimen_ids=None):
         '''
 
         # starting in version 2.0, neuropil correction follows trace demixing
-        if self.pipeline_version >= parse_version("2.0"):
+        if self.pipeline_version >= Version("2.0"):
             timestamps, cell_traces = self.get_demixed_traces(cell_specimen_ids)
         else:
             timestamps, cell_traces = self.get_fluorescence_traces(cell_specimen_ids)