Drop Python 3.7 support (#897)

hdmf-dev · Jul 10, 2023 · 6808826 · 6808826
1 parent 0d477f5
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -62,7 +62,6 @@ body:
     attributes:
       label: Python Version
       options:
-        - "3.7"
         - "3.8"
         - "3.9"
         - "3.10"

diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -22,24 +22,21 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: linux-python3.8              , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: linux-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
           - { name: linux-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
           - { name: linux-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
           - { name: linux-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-python3.11-optional    , test-tox-env: py311-optional  , build-tox-env: build-py311-optional  , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-python3.11-upgraded    , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-python3.11-prerelease  , test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, python-ver: "3.11", os: ubuntu-latest }
-          - { name: windows-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: windows-latest }
-          - { name: windows-python3.8            , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: windows-latest }
           - { name: windows-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: windows-latest }
           - { name: windows-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: windows-latest }
           - { name: windows-python3.11           , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: windows-latest }
           - { name: windows-python3.11-optional  , test-tox-env: py311-optional  , build-tox-env: build-py311-optional  , python-ver: "3.11", os: windows-latest }
           - { name: windows-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: windows-latest }
           - { name: windows-python3.11-prerelease, test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, python-ver: "3.11", os: windows-latest }
-          - { name: macos-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: macos-latest }
-          - { name: macos-python3.8              , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: macos-latest }
           - { name: macos-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: macos-latest }
           - { name: macos-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: macos-latest }
           - { name: macos-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: macos-latest }
@@ -92,13 +89,13 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.7-minimum      , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: linux-gallery-python3.8-minimum      , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
           - { name: linux-gallery-python3.11-upgraded    , test-tox-env: gallery-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-gallery-python3.11-prerelease  , test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: ubuntu-latest }
-          - { name: windows-gallery-python3.7-minimum    , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: windows-latest }
+          - { name: windows-gallery-python3.8-minimum    , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: windows-latest }
           - { name: windows-gallery-python3.11-upgraded  , test-tox-env: gallery-py311-upgraded  , python-ver: "3.11", os: windows-latest }
           - { name: windows-gallery-python3.11-prerelease, test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: windows-latest }
-          - { name: macos-gallery-python3.7-minimum      , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: macos-latest }
+          - { name: macos-gallery-python3.8-minimum      , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: macos-latest }
           - { name: macos-gallery-python3.11-upgraded    , test-tox-env: gallery-py311-upgraded  , python-ver: "3.11", os: macos-latest }
           - { name: macos-gallery-python3.11-prerelease  , test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: macos-latest }
     steps:
@@ -138,8 +135,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: conda-linux-python3.8            , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: conda-linux-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
           - { name: conda-linux-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
           - { name: conda-linux-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
           - { name: conda-linux-python3.11           , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
@@ -168,8 +164,7 @@ jobs:
         run: |
           conda config --set always_yes yes --set changeps1 no
           conda info
-          # the conda dependency resolution for tox under python 3.7 can install the wrong importlib_metadata
-          conda install -c conda-forge tox "importlib_metadata>4"
+          conda install -c conda-forge tox
 
       - name: Conda reporting
         run: |

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -19,13 +19,13 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: linux-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
           - { name: linux-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
           # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
           - { name: linux-python3.11-upgraded    , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest , upload-wheels: true }
-          - { name: windows-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: windows-latest }
+          - { name: windows-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: windows-latest }
           - { name: windows-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: windows-latest }
-          - { name: macos-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: macos-latest }
+          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: macos-latest }
           - { name: macos-python3.11-upgraded    , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
@@ -80,9 +80,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.7-minimum    , test-tox-env: gallery-py37-minimum  , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: linux-gallery-python3.8-minimum    , test-tox-env: gallery-py38-minimum  , python-ver: "3.8" , os: ubuntu-latest }
           - { name: linux-gallery-python3.11-upgraded  , test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: ubuntu-latest }
-          - { name: windows-gallery-python3.7-minimum  , test-tox-env: gallery-py37-minimum  , python-ver: "3.7" , os: windows-latest }
+          - { name: windows-gallery-python3.8-minimum  , test-tox-env: gallery-py38-minimum  , python-ver: "3.8" , os: windows-latest }
           - { name: windows-gallery-python3.11-upgraded, test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: windows-latest }
     steps:
       - name: Cancel non-latest runs
@@ -120,7 +120,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: conda-linux-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
           - { name: conda-linux-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
@@ -144,8 +144,7 @@ jobs:
         run: |
           conda config --set always_yes yes --set changeps1 no
           conda info
-          # the conda dependency resolution for tox under python 3.7 can install the wrong importlib_metadata
-          conda install -c conda-forge tox "importlib_metadata>4"
+          conda install -c conda-forge tox
 
       - name: Conda reporting
         run: |

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,12 +1,13 @@
 # HDMF Changelog
 
-## HMDF 3.6.2 (Upcoming)
+## HMDF 3.7.0 (Upcoming)
 
 ### New features and minor improvements
 - Updated `ExternalResources` to have EntityKeyTable with updated tests/documentation and minor bug fix to ObjectKeyTable. @mavaylon1 [#872](https://github.com/hdmf-dev/hdmf/pull/872)
 - Added warning for DynamicTableRegion links that are not added to the same parent as the original container object. @mavaylon1 [#891](https://github.com/hdmf-dev/hdmf/pull/891)
 - Added the `TermSet` class along with integrated validation methods for any child of `AbstractContainer`, e.g., `VectorData`, `Data`, `DynamicTable`. @mavaylon1 [#880](https://github.com/hdmf-dev/hdmf/pull/880)
 - Updated `HDMFIO` and `HDF5IO` to support `ExternalResources`. @mavaylon1 [#895](https://github.com/hdmf-dev/hdmf/pull/895)
+- Dropped Python 3.7 support. @rly [#897](https://github.com/hdmf-dev/hdmf/pull/897)
 
 ### Documentation and tutorial enhancements:
 

diff --git a/docs/source/install_users.rst b/docs/source/install_users.rst
@@ -4,7 +4,7 @@
 Installing HDMF
 ---------------
 
-HDMF requires having Python 3.7, 3.8, 3.9, 3.10, or 3.11 installed. If you don't have Python installed and want the simplest way to
+HDMF requires having Python 3.8, 3.9, 3.10, or 3.11 installed. If you don't have Python installed and want the simplest way to
 get started, we recommend you install and use the `Anaconda Distribution`_. It includes Python, NumPy, and many other
 commonly used packages for scientific computing and data science.
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -13,11 +13,10 @@ authors = [
 ]
 description = "A hierarchical data modeling framework for modern science data standards"
 readme = "README.rst"
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 license = {text = "BSD-3-Clause"}
 classifiers = [
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
@@ -32,11 +31,10 @@ classifiers = [
 dependencies = [
     "h5py>=2.10",
     "jsonschema>=2.6.0",
-    "numpy>=1.16",
+    "numpy>=1.18",
     "pandas>=1.0.5",
     "ruamel.yaml>=0.16",
-    "scipy>=1.1",
-    "importlib-metadata<4.3; python_version < '3.8'",  # TODO: remove when minimum python version is 3.8
+    "scipy>=1.4",
     "importlib-resources; python_version < '3.9'",  # TODO: remove when minimum python version is 3.9
 ]
 dynamic = ["version"]

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -5,11 +5,9 @@
 black==23.3.0
 codespell==2.2.4
 coverage==7.2.5
-pre-commit==3.3.1; python_version >= "3.8"
-pre-commit==2.21.0; python_version < "3.8"  # pre-commit 3 dropped python 3.7 support
+pre-commit==3.3.1
 pytest==7.3.1
 pytest-cov==4.0.0
 python-dateutil==2.8.2
 ruff==0.0.265
-tox==4.5.1; python_version >= "3.8"
-tox==3.28.0; python_version < "3.8"  # tox 4+ has virtualenv requirements that are incompatible with other pkgs
+tox==4.5.1
diff --git a/requirements-min.txt b/requirements-min.txt
@@ -1,12 +1,11 @@
 # minimum versions of package dependencies for installing HDMF
 h5py==2.10  # support for selection of datasets with list of indices added in 2.10
-importlib-metadata==4.2.0; python_version < "3.8"  # TODO: remove when minimum python version is 3.8
 importlib-resources==5.12.0; python_version < "3.9"  # TODO: remove when when minimum python version is 3.9
 jsonschema==3.2.0
-numpy==1.16  # numpy>=1.16,<1.18 does not provide wheels for python 3.8 and does not build well on windows
+numpy==1.18
 pandas==1.0.5  # when this is changed to >=1.5.0, see TODO items referenced in #762
 ruamel.yaml==0.16
-scipy==1.1  # scipy>=1.1,<1.4 does not provide wheels for python 3.8 and building scipy can fail due to incompatibilities with numpy
+scipy==1.4
 linkml-runtime==1.5.0
 tqdm==4.41.0
 zarr==2.12.0
diff --git a/requirements.txt b/requirements.txt
@@ -1,13 +1,8 @@
 # pinned dependencies to reproduce an entire development environment to use HDMF
-# note that python 3.7 end of life is 27 Jun 2023
 h5py==3.8.0
-importlib-metadata==4.2.0; python_version < "3.8"  # TODO: remove when minimum python version is 3.8
 importlib-resources==5.12.0; python_version < "3.9"  # TODO: remove when when minimum python version is 3.9
 jsonschema==4.17.3
-numpy==1.24.3; python_version >= "3.8"
-numpy==1.21.5; python_version < "3.8"  # numpy 1.22 dropped python 3.7 support
-pandas==2.0.1; python_version >= "3.8"
-pandas==1.3.5; python_version < "3.8"  # pandas 1.4 dropped python 3.7 support
+numpy==1.24.3
+pandas==2.0.1
 ruamel.yaml==0.17.24
-scipy==1.10.1; python_version >= "3.8"
-scipy==1.7.3; python_version < "3.8"   # scipy 1.8 dropped python 3.7 support
+scipy==1.10.1
diff --git a/src/hdmf/__init__.py b/src/hdmf/__init__.py
@@ -27,11 +27,7 @@ def get_region_slicer(**kwargs):
     return None
 
 
-try:
-    from importlib.metadata import version  # noqa: E402
-except ImportError:
-    # TODO: Remove when python 3.8 becomes the new minimum
-    from importlib_metadata import version  # noqa: E402
+from importlib.metadata import version  # noqa: E402
 
 __version__ = version(__package__)
 del version

diff --git a/src/hdmf/data_utils.py b/src/hdmf/data_utils.py
@@ -1,7 +1,5 @@
 import copy
 import math
-import functools  # TODO: remove when Python 3.7 support is dropped - see #785
-import operator  # TODO: remove when Python 3.7 support is dropped
 from abc import ABCMeta, abstractmethod
 from collections.abc import Iterable
 from warnings import warn
@@ -237,15 +235,11 @@ def __init__(self, **kwargs):
             f"evenly divide the buffer shape ({self.buffer_shape})!"
         )
 
-        # TODO: replace with below when Python 3.7 support is dropped
-        # self.num_buffers = math.prod(
-        self.num_buffers = functools.reduce(
-            operator.mul,
+        self.num_buffers = math.prod(
             [
                 math.ceil(maxshape_axis / buffer_axis)
                 for buffer_axis, maxshape_axis in zip(self.buffer_shape, self.maxshape)
             ],
-            1,
         )
         self.buffer_selection_generator = (
             tuple(
@@ -311,15 +305,11 @@ def _get_default_chunk_shape(self, **kwargs) -> Tuple[int, ...]:
 
         min_maxshape = min(self.maxshape)
         v = tuple(math.floor(maxshape_axis / min_maxshape) for maxshape_axis in self.maxshape)
-        # TODO: replace with below when Python 3.7 support is dropped
-        # prod_v = math.prod(v)
-        prod_v = functools.reduce(operator.mul, v, 1)
+        prod_v = math.prod(v)
         while prod_v * itemsize > chunk_bytes and prod_v != 1:
             non_unit_min_v = min(x for x in v if x != 1)
             v = tuple(math.floor(x / non_unit_min_v) if x != 1 else x for x in v)
-            # TODO: replace with below when Python 3.7 support is dropped
-            # prod_v = math.prod(v)
-            prod_v = functools.reduce(operator.mul, v, 1)
+            prod_v = math.prod(v)
         k = math.floor((chunk_bytes / (prod_v * itemsize)) ** (1 / n_dims))
         return tuple([min(k * x, self.maxshape[dim]) for dim, x in enumerate(v)])
 
@@ -346,9 +336,7 @@ def _get_default_buffer_shape(self, **kwargs) -> Tuple[int, ...]:
 
         k = math.floor(
             (
-                # TODO: replace with below when Python 3.7 support is dropped
-                # buffer_gb * 1e9 / (math.prod(self.chunk_shape) * self.dtype.itemsize)
-                buffer_gb * 1e9 / (functools.reduce(operator.mul, self.chunk_shape, 1) * self.dtype.itemsize)
+                buffer_gb * 1e9 / (math.prod(self.chunk_shape) * self.dtype.itemsize)
             ) ** (1 / len(self.chunk_shape))
         )
         return tuple(

diff --git a/tox.ini b/tox.ini
@@ -4,7 +4,7 @@
 # and then run "tox" from this directory.
 
 [tox]
-envlist = py37, py38, py39, py310, py311
+envlist = py38, py39, py310, py311
 requires = pip >= 22.0
 
 [testenv]
@@ -52,9 +52,9 @@ deps =
     -rrequirements-opt.txt
 commands = {[testenv]commands}
 
-# Test with python 3.7; pinned dev reqs; minimum run reqs
-[testenv:py37-minimum]
-basepython = python3.7
+# Test with python 3.8; pinned dev reqs; minimum run reqs
+[testenv:py38-minimum]
+basepython = python3.8
 deps =
     -rrequirements-dev.txt
     -rrequirements-min.txt
@@ -66,10 +66,6 @@ commands =
     python -m pip install --upgrade build
     python -m build
 
-[testenv:build-py37]
-basepython = python3.7
-commands = {[testenv:build]commands}
-
 [testenv:build-py38]
 basepython = python3.8
 commands = {[testenv:build]commands}
@@ -111,8 +107,8 @@ deps =
     -rrequirements-opt.txt
 commands = {[testenv:build]commands}
 
-[testenv:build-py37-minimum]
-basepython = python3.7
+[testenv:build-py38-minimum]
+basepython = python3.8
 deps =
     -rrequirements-dev.txt
     -rrequirements-min.txt
@@ -178,9 +174,9 @@ deps =
     -rrequirements-opt.txt
 commands = {[testenv:gallery]commands}
 
-# Test with python 3.7; pinned dev and doc reqs; minimum run reqs
-[testenv:gallery-py37-minimum]
-basepython = python3.7
+# Test with python 3.8; pinned dev and doc reqs; minimum run reqs
+[testenv:gallery-py38-minimum]
+basepython = python3.8
 deps =
     -rrequirements-dev.txt
     -rrequirements-min.txt