Bump the pip-version group with 3 updates (#1004)

* Bump the pip-version group with 3 updates

Bumps the pip-version group with 3 updates: [coverage](https://github.com/nedbat/coveragepy), [numpy](https://github.com/numpy/numpy) and [tables](https://github.com/PyTables/PyTables).


Updates `coverage` from 7.6.0 to 7.6.1
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](nedbat/coveragepy@7.6.0...7.6.1)

Updates `numpy` from 2.0.1 to 2.1.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.0.1...v2.1.0)

Updates `tables` from 3.9.2 to 3.10.1
- [Release notes](https://github.com/PyTables/PyTables/releases)
- [Changelog](https://github.com/PyTables/PyTables/blob/master/RELEASE_NOTES.rst)
- [Commits](PyTables/PyTables@v3.9.2...v3.10.1)

---
updated-dependencies:
- dependency-name: coverage
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip-version
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip-version
- dependency-name: tables
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip-version
...

Signed-off-by: dependabot[bot] <[email protected]>

* Test Python 3.9 on oldest dependencies

* Update oldest numpy to 1.19.3 for maintenance release

* Require pandas>=1.2.0 to ensure Python 3.9 wheels are available.

* Require h5py>=3.0.0 to ensure Python 3.9 wheels are available.

* Bump tqdm requirement due to bug in older versions not supporting Python 3.9.

A bug with `setcheckinterval` (removed in Python 3.9) was fixed in
https://github.com/tqdm/tqdm/releases/tag/v4.46.1

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Corwin Kerr <[email protected]>
Co-authored-by: Bradley Dice <[email protected]>

.github/workflows/ci-oldest-reqs.txt

@@ -1,15 +1,15 @@
 click==7.1.2
 coverage==5.3.1
 filelock==3.0.0
-h5py==2.10.0; platform_machine != "arm64" or platform_system != "Darwin"
+h5py==3.0.0; platform_machine != "arm64" or platform_system != "Darwin"
 h5py==3.7.0; platform_machine == "arm64" or platform_system == "Darwin"
-numpy==1.19.0; platform_machine != "arm64" or platform_system != "Darwin"
+numpy==1.19.3; platform_machine != "arm64" or platform_system != "Darwin"
 numpy==1.21.0; platform_machine == "arm64" and platform_system == "Darwin"
 packaging==15.0
-pandas==1.0.0; platform_machine != "arm64" or platform_system != "Darwin"
+pandas==1.2.0; platform_machine != "arm64" or platform_system != "Darwin"
 pandas==1.4.0; platform_machine == "arm64" and platform_system == "Darwin"
 pytest==6.2.1
 pytest-cov==2.10.1
 pytest-xdist==2.5.0
 tables==3.6.1; platform_machine != "arm64" or platform_system != "Darwin"
-tqdm==4.10.0
+tqdm==4.46.1

.github/workflows/run-pytest.yml

@@ -31,6 +31,8 @@ jobs:
           # Oldest dependency tests
           - python: '3.8'
             dependencies: 'oldest'
+          - python: '3.9'
+            dependencies: 'oldest'
           - os: 'macos-latest'
             python: '3.8'
             dependencies: 'oldest'

pyproject.toml

@@ -39,7 +39,7 @@ dependencies = [
     # Synced collections for signac's backend
     "synced_collections>=1.0.0",
     # Progress bars
-    "tqdm>=4.10.0",
+    "tqdm>=4.46.1",
 ]
 
 [project.optional-dependencies]

requirements.txt

@@ -1,4 +1,4 @@
 filelock>=3.0
 packaging>=15.0
 synced_collections>=1.0.0
-tqdm>=4.10.0
+tqdm>=4.46.1

requirements/requirements-test-optional.txt

@@ -1,4 +1,4 @@
 h5py==3.11.0; implementation_name=='cpython'
-numpy==2.0.1
+numpy==2.1.0
 pandas==2.2.2; implementation_name=='cpython'
-tables==3.9.2; implementation_name=='cpython' and platform_machine != "arm64" or platform_system != "Darwin"
+tables==3.10.1; implementation_name=='cpython' and platform_machine != "arm64" or platform_system != "Darwin"

requirements/requirements-test.txt

@@ -1,4 +1,4 @@
-coverage==7.6.0
+coverage==7.6.1
 pytest==8.3.2
 pytest-cov==5.0.0
 pytest-xdist==3.6.1