Updated installation instructions

.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

.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

.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

.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: |

.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: |

.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: |

.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

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:**

MANIFEST.in

@@ -1,2 +1 @@
-include hed/_version.py
-include requirements.txt
+include hed/_version.py

README.md

@@ -245,21 +245,19 @@ 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
 
 # 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
 ```
 

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/
 ```
 

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**

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"

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]