Update docs, change optional deps group

.github/PULL_REQUEST_TEMPLATE/release.md

@@ -2,10 +2,8 @@ Prepare for release of HDMF-Zarr [version]
 
 ### Before merging:
 - [ ] Make sure all PRs to be included in this release have been merged to `dev`.
-- [ ] Major and minor releases: Update package versions in `requirements.txt`, `requirements-dev.txt`,
-  `requirements-doc.txt`, and `requirements-opt.txt` to the latest versions,
-  and update dependency ranges in `pyproject.toml` and minimums in `requirements-min.txt` as needed.
-  Run `pip install pur && pur -r -d [requirements file]` to see which packages can be updated.
+- [ ] Major and minor releases: Update dependency ranges in `pyproject.toml` and minimums in 
+  `requirements-min.txt` as needed.
 - [ ] Check legal file dates and information in `Legal.txt`, `license.txt`, `README.rst`, `docs/source/conf.py`,
   and any other locations as needed
 - [ ] Update `pyproject.toml` as needed
@@ -27,5 +25,5 @@ Prepare for release of HDMF-Zarr [version]
 4. Either monitor [conda-forge/hdmf_zarr-feedstock](https://github.com/conda-forge/hdmf_zarr-feedstock) for the
    regro-cf-autotick-bot bot to create a PR updating the version of HDMF to the latest PyPI release, usually within
    24 hours of release, or manually create a PR updating `recipe/meta.yaml` with the latest version number
-   and SHA256 retrieved from PyPI > HDMF-Zarr > Download Files > View hashes for the `.tar.gz` file. Re-render and update
-   dependencies as needed.
+   and SHA256 retrieved from PyPI > HDMF-Zarr > Download Files > View hashes for the `.tar.gz` file. Re-render and 
+   update the dependencies as needed.

.github/workflows/HDMF_dev.yaml

@@ -19,8 +19,7 @@ jobs:
 
       - name: Install HDMF_Zarr Requirements
         run: |
-          python -m pip install -r requirements-dev.txt -r requirements.txt
-          pip install .
+          python -m pip install ".[test]"
           
       - name: Clone and Install HDMF Dev Branch
         run: |

.github/workflows/check_external_links.yml

@@ -23,8 +23,7 @@ jobs:
       - name: Install Sphinx dependencies and package
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements-doc.txt -r requirements.txt -r requirements-opt.txt
-          python -m pip install .
+          python -m pip install ".[test,docs,full]"
 
       - name: Check Sphinx external links
         run: sphinx-build -W -b linkcheck ./docs/source ./test_build

.github/workflows/run_coverage.yml

@@ -41,29 +41,30 @@ jobs:
         with:
           python-version: ${{ env.PYTHON }}
 
-      - name: Install dependencies
+      - name: Upgrade pip
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements-dev.txt -r requirements.txt
-
-      - name: Install optional dependencies
-        if: ${{ matrix.opt_req }}
-        run: python -m pip install -r requirements-opt.txt
 
       - name: Install package
+        if: ! ${{ matrix.opt_req }}
         run: |
-          python -m pip install .
-          python -m pip list
+          python -m pip install ".[test]"
+
+      - name: Install package with optional dependencies
+        if: ${{ matrix.opt_req }}
+        run: python -m pip install ".[test,full]"
 
       - name: Run tests and generate coverage report
         run: |
           # coverage is configured in pyproject.toml
-          pytest --cov --cov-report=xml --cov-report=term  # codecov uploader requires xml format
+          # codecov uploader requires xml format
+          python -m pip list
+          pytest --cov --cov-report=xml --cov-report=term
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
-          file: ./coverage.xml
+          files: ./coverage.xml
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.readthedocs.yaml

@@ -24,7 +24,7 @@ formats: all
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-    - path: .[docs,tqdm,fsspec,s3fs] # path to the package relative to the root
+    - path: .[docs,full] # path to the package relative to the root
 
 # Optionally include all submodules
 submodules:

docs/source/installation.rst

@@ -24,14 +24,15 @@ For Developers
 Install hdmf-zarr from GitHub
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The following illustrates how to install both ``hdmf`` and ``hdfm_zarr`` from GitHub
-in a Conda environment. Normally we don't need to install ``hdmf`` directly, but until
-``hdmf 3.4.0`` is released we need to use the ``dev`` version of ``hdmf``.
+The following illustrates how to install both ``hdmf`` and ``hdmf_zarr`` from GitHub
+in a Conda environment, with all of the optional, testing, and documentation dependencies
+for hdmf-zarr. Normally, we don't need to install ``hdmf`` directly, but it is
+often useful to use the ``dev`` branch of the ``hdmf`` GitHub repository.
 
 .. code-block::
 
-    conda create --name hdmf-zarr-test python=3.9
-    conda activate hdmf-zarr-test
+    conda create --name hdmf-zarr-dev python=3.13
+    conda activate hdmf-zarr-dev
 
     git clone --recurse-submodules https://github.com/hdmf-dev/hdmf.git
     cd hdmf
@@ -41,12 +42,11 @@ in a Conda environment. Normally we don't need to install ``hdmf`` directly, but
 
     git clone https://github.com/hdmf-dev/hdmf-zarr.git
     cd hdmf-zarr
-    pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt
-    pip install -e .
+    pip install -e ".[all]"
 
 .. note::
 
-   Depending on versions, it is possible that when installing ``hdmf-zarr`` that pip will
+   Depending on versions, it is possible that when installing ``hdmf-zarr``, that ``pip`` will
    install HDMF directly from PyPI instead of using the development version of HDMF
    that is already installed. In that case call ``pip uninstall hdmf`` and
    go to the ``hdmf`` directory and run ``pip install -e .`` again

pyproject.toml

@@ -38,9 +38,12 @@ dependencies = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
-tqdm = ["tqdm>=4.41.0"]
-fsspec = ["fsspec"]
-s3fs = ["s3fs"]
+# all optional dependencies
+full = [
+    "tqdm>=4.41.0",
+    "fsspec",
+    "s3fs",
+]
 
 # development dependencies
 test = [
@@ -54,6 +57,7 @@ test = [
     "tox",
 ]
 
+# documentation dependencies
 docs = [
     "matplotlib",
     "sphinx>=4",  # improved support for docutils>=0.17
@@ -62,6 +66,10 @@ docs = [
     "sphinx-copybutton",
 ]
 
+# all possible dependencies
+all = ["hdmf-zarr[full,test,docs]"]
+
+
 [project.urls]
 "Homepage" = "https://github.com/hdmf-dev/hdmf-zarr"
 "Bug Tracker" = "https://github.com/hdmf-dev/hdmf-zarr/issues"

tox.ini

@@ -37,14 +37,14 @@ commands = {[testenv]commands}
 
 # Test with python 3.13 and all optional dependencies
 [testenv:py313-optional]
-extras = {[testenv]extras}, tqdm, fsspec, s3fs
+extras = {[testenv]extras}, full
 commands = {[testenv]commands}
 
 # Test with python 3.13 and all optional dependencies, using pre-release versions
 [testenv:py313-prerelease]
 install_command =
     python -m pip install -U --pre {opts} {packages}
-extras = {[testenv]extras}, tqdm, fsspec, s3fs
+extras = {[testenv]extras}, full
 commands = {[testenv]commands}
 
 # Test with python 3.9 and minimum dependencies
@@ -87,14 +87,14 @@ commands = {[testenv:gallery]commands}
 
 # Test with python 3.13 and all optional dependencies
 [testenv:gallery-py313-optional]
-extras = {[testenv:gallery]extras}, tqdm, fsspec, s3fs
+extras = {[testenv:gallery]extras}, full
 commands = {[testenv:gallery]commands}
 
 # Test with python 3.13 and all optional dependencies, using pre-release versions
 [testenv:gallery-py313-prerelease]
 install_command =
     python -m pip install -U --pre {opts} {packages}
-extras = {[testenv:gallery]extras}, tqdm, fsspec, s3fs
+extras = {[testenv:gallery]extras}, full
 commands = {[testenv:gallery]commands}
 
 # Test with python 3.9 and minimum dependencies