From 616f29cfe566520a3e33aa38320e19a46884a9c6 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Wed, 4 Feb 2026 14:59:22 -0600 Subject: [PATCH] Updated installation instructions --- .github/workflows/ci.yaml | 6 ++---- .github/workflows/ci_cov.yaml | 4 ++-- .github/workflows/ci_windows.yaml | 3 +-- .github/workflows/docs.yaml | 5 ++--- .github/workflows/links.yaml | 3 +-- .github/workflows/notebook_tests.yaml | 5 +---- .github/workflows/spec_tests.yaml | 1 - CONTRIBUTING.md | 5 +---- MANIFEST.in | 3 +-- README.md | 12 +++++------ docs/overview.md | 3 +-- docs/requirements.txt | 6 ------ docs/user_guide.md | 3 +-- hed/_version.py | 6 +++--- pyproject.toml | 17 ++++++--------- requirements-dev.txt | 30 --------------------------- requirements.txt | 10 --------- 17 files changed, 27 insertions(+), 95 deletions(-) delete mode 100644 docs/requirements.txt delete mode 100644 requirements-dev.txt delete mode 100644 requirements.txt diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index feea8e59..a1f0183b 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -50,15 +50,13 @@ jobs: - uses: actions/cache@v5 with: path: ${{ env.pythonLocation }} - key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('docs/requirements.txt') }} + key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} # Install dependencies - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r requirements.txt - pip install -r docs/requirements.txt - pip install -e .[test] + pip install -e .[docs,test] # Run spec tests without coverage for non Python 3.10 - name: Run spec_test diff --git a/.github/workflows/ci_cov.yaml b/.github/workflows/ci_cov.yaml index 5cd67125..b6d3d0b6 100644 --- a/.github/workflows/ci_cov.yaml +++ b/.github/workflows/ci_cov.yaml @@ -32,8 +32,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install ruff -r requirements.txt -r docs/requirements.txt - pip install -e .[test] + pip install ruff + pip install -e .[docs,test] # Run ruff - name: Lint with ruff diff --git a/.github/workflows/ci_windows.yaml b/.github/workflows/ci_windows.yaml index a9550956..55eb57e3 100644 --- a/.github/workflows/ci_windows.yaml +++ b/.github/workflows/ci_windows.yaml @@ -28,12 +28,11 @@ jobs: - uses: actions/cache@v5 with: path: ${{ env.pythonLocation }} - key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('docs/requirements.txt') }} + key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r requirements.txt pip install -e .[test] - name: Test with unittest diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 2e0554d5..0c32c452 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -32,15 +32,14 @@ jobs: uses: actions/cache@v5 with: path: ~/.cache/pip - key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} + key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }} restore-keys: | ${{ runner.os }}-pip- - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r docs/requirements.txt - pip install -e . + pip install -e .[docs] - name: Configure Git for GitHub Pages run: | diff --git a/.github/workflows/links.yaml b/.github/workflows/links.yaml index 3113a59e..c68dfbfc 100644 --- a/.github/workflows/links.yaml +++ b/.github/workflows/links.yaml @@ -28,8 +28,7 @@ jobs: - name: Install dependencies run: | pip install --upgrade pip - pip install -r docs/requirements.txt - pip install -e . + pip install -e .[docs] - name: Build documentation with Sphinx run: | diff --git a/.github/workflows/notebook_tests.yaml b/.github/workflows/notebook_tests.yaml index 4becd388..10bc09d5 100644 --- a/.github/workflows/notebook_tests.yaml +++ b/.github/workflows/notebook_tests.yaml @@ -40,10 +40,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r requirements.txt - pip install -e . - # Install Jupyter dependencies for running notebooks - pip install jupyter notebook nbformat nbconvert ipykernel + pip install -e .[examples] - name: Test notebook structure and imports run: | diff --git a/.github/workflows/spec_tests.yaml b/.github/workflows/spec_tests.yaml index ca39bd7b..47249979 100644 --- a/.github/workflows/spec_tests.yaml +++ b/.github/workflows/spec_tests.yaml @@ -29,7 +29,6 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade --upgrade-strategy eager pip - pip install -r requirements.txt pip install -e .[test] - name: Spec Error Tests diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 5c0b09d9..e319587e 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -55,10 +55,7 @@ This project adheres to a code of conduct that we expect all contributors to fol 3. **Install in development mode:** ```bash - pip install -e . - pip install -r requirements.txt - pip install -r docs/requirements.txt - pip install -e .[dev] # Install development tools (black, ruff, codespell) + pip install -e .[dev,test,docs,examples] ``` 4. **Run tests to verify setup:** diff --git a/MANIFEST.in b/MANIFEST.in index fe6aa87a..ceb19c81 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,2 +1 @@ -include hed/_version.py -include requirements.txt \ No newline at end of file +include hed/_version.py \ No newline at end of file diff --git a/README.md b/README.md index 6c68eaa6..53bf532e 100644 --- a/README.md +++ b/README.md @@ -245,13 +245,11 @@ We welcome contributions! Here's how you can help: git clone https://github.com/hed-standard/hed-python.git cd hed-python -# Install in development mode with all dependencies (including Jupyter) -pip install -e .[examples] -pip install -r requirements-dev.txt +# Install in development mode with all dependencies +pip install -e .[dev,test,docs,examples] -# Or just core development dependencies -pip install -e . -pip install -r requirements.txt +# Or just core + test dependencies +pip install -e .[test] # Run tests python -m unittest discover tests @@ -259,7 +257,7 @@ python -m unittest discover tests # Run specific test file python -m unittest tests/path/to/test_file.py -# Test notebooks (requires Jupyter dependencies) +# Test notebooks (requires examples dependencies) python -m unittest tests.test_notebooks ``` diff --git a/docs/overview.md b/docs/overview.md index e29c21d4..f3d137b9 100644 --- a/docs/overview.md +++ b/docs/overview.md @@ -76,8 +76,7 @@ The example notebooks are only available in the GitHub repository. Choose one of ```bash git clone https://github.com/hed-standard/hed-python.git cd hed-python -pip install -r requirements.txt -pip install jupyter notebook +pip install -e .[examples] # Notebooks are in: examples/ ``` diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 7da139d8..00000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,6 +0,0 @@ -sphinx>=7.1.0,<10.0 -furo>=2024.1.29 -sphinx-copybutton>=0.5.2 -myst-parser>=3.0.0 -sphinx-autodoc-typehints>=1.24.0 -linkify-it-py>=2.0.3 diff --git a/docs/user_guide.md b/docs/user_guide.md index a39d6db3..c82c5f3c 100644 --- a/docs/user_guide.md +++ b/docs/user_guide.md @@ -286,8 +286,7 @@ The [examples](https://github.com/hed-standard/hed-python/tree/main/examples) di ```bash git clone https://github.com/hed-standard/hed-python.git cd hed-python -pip install -r requirements.txt -pip install jupyter notebook +pip install -e .[examples] ``` **Option 2: Download just the examples** diff --git a/hed/_version.py b/hed/_version.py index a73dde96..a5acb779 100644 --- a/hed/_version.py +++ b/hed/_version.py @@ -28,7 +28,7 @@ commit_id: COMMIT_ID __commit_id__: COMMIT_ID -__version__ = version = "0.9.0.post1.dev15+g972098b2e.d20260203" -__version_tuple__ = version_tuple = (0, 9, 0, "post1", "dev15", "g972098b2e.d20260203") +__version__ = version = "0.9.0.post1.dev20+gd67e5991c.d20260204" +__version_tuple__ = version_tuple = (0, 9, 0, "post1", "dev20", "gd67e5991c.d20260204") -__commit_id__ = commit_id = "g972098b2e" +__commit_id__ = commit_id = "gd67e5991c" diff --git a/pyproject.toml b/pyproject.toml index 9056a33c..9a7a05d3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,18 +42,13 @@ requires-python = ">=3.10" dependencies = [ "click>=8.0.0", "click-option-group>=0.5.0", - "defusedxml", - "et-xmlfile", - "inflect", - "jsonschema", - "numpy", - "openpyxl", + "defusedxml>=0.7.1", + "inflect>=7.5.0", + "numpy>=2.0.2", + "openpyxl>=3.1.5", "pandas>=2.2.3,<3.0.0", - "portalocker", - "python-dateutil", - "pytz", - "semantic-version", - "six" + "portalocker>=3.1.1", + "semantic-version>=2.10.0" ] [project.urls] diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index df5abf25..00000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,30 +0,0 @@ -# Requirements for development and testing -# Install with: pip install -r requirements-dev.txt - -# Core package requirements (from requirements.txt) --r requirements.txt - -# Testing requirements -coverage>=7.0.0 - -# Code quality tools -ruff>=0.8.0 -codespell>=2.2.0 -black[jupyter]>=26.1.0 -mdformat>=0.7.0 -mdformat-myst>=0.1.5 - -# Documentation requirements -sphinx>=7.1.0,<10.0 -furo>=2024.1.29 -sphinx-copybutton>=0.5.2 -myst-parser>=3.0.0 -sphinx-autodoc-typehints>=1.24.0 -linkify-it-py>=2.0.3 - -# Jupyter notebook requirements for examples -jupyter>=1.0.0 -notebook>=7.0.0 -nbformat>=5.9.0 -nbconvert>=7.0.0 -ipykernel>=6.25.0 diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 77a02e24..00000000 --- a/requirements.txt +++ /dev/null @@ -1,10 +0,0 @@ -click>=8.0.0 -click-option-group>=0.5.0 -defusedxml>=0.7.1 -inflect>=7.5.0 -jsonschema>=4.23.0 -numpy>=2.0.2 -openpyxl>=3.1.5 -pandas>=2.2.3,<3.0.0 -portalocker>=3.1.1 -semantic-version>=2.10.0