diff --git a/.github/workflows/build_and_deploy_mac.yml b/.github/workflows/build_and_deploy_mac.yml
index d1bee1eda..488dbe73d 100644
--- a/.github/workflows/build_and_deploy_mac.yml
+++ b/.github/workflows/build_and_deploy_mac.yml
@@ -8,33 +8,48 @@ on:
jobs:
deploy-on-mac:
runs-on: macos-15-intel
- # NOTE: if changing this to macos-latest (arm64), make sure to use the apple-silicon conda environment.
defaults:
run:
- shell: bash -l {0}
+ shell: bash
steps:
- uses: actions/checkout@v6
- - name: Set up conda
- uses: conda-incubator/setup-miniconda@v3
+ - name: Install uv
+ uses: astral-sh/setup-uv@v8.3.2
with:
- miniforge-version: latest
- activate-environment: nwb-guide
- conda-remove-defaults: true
+ enable-cache: true
- - name: Create and activate environment
- run: conda env update --name nwb-guide --file environments/environment-MAC-intel.yml
+ - name: Install Python dependencies
+ run: uv sync --locked
+
+ - name: Add the virtual environment to PATH
+ run: |
+ if [ "$RUNNER_OS" == "Windows" ]; then
+ echo "$GITHUB_WORKSPACE\\.venv\\Scripts" >> "$GITHUB_PATH"
+ else
+ echo "$GITHUB_WORKSPACE/.venv/bin" >> "$GITHUB_PATH"
+ fi
+ echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> "$GITHUB_ENV"
- name: Use Node.js 20
uses: actions/setup-node@v6
with:
node-version: 20
+ cache: 'npm'
- name: Install package.json modules and their dependencies (not via `npm ci`)
run: npm install --verbose
+ # Keep the released bundle consistent with the one exercised by the build tests.
+ # matplotlib arrives transitively through neuroconv's extras and GUIDE never imports it.
+ # PyInstaller bundles whatever is installed, and matplotlib's hidden libraries break the
+ # packaged build, so every job drops it to keep tests and releases on the same environment.
+ # `uv tree --invert --package matplotlib` lists what currently pulls it in.
+ - name: Manually remove matplotlib
+ run: uv pip uninstall matplotlib || true
+
- uses: apple-actions/import-codesign-certs@v6
with:
# Currently this is set to Ryan's Developer ID certificate
diff --git a/.github/workflows/build_and_deploy_win.yml b/.github/workflows/build_and_deploy_win.yml
index 90c75d735..77e4f28e9 100644
--- a/.github/workflows/build_and_deploy_win.yml
+++ b/.github/workflows/build_and_deploy_win.yml
@@ -10,28 +10,44 @@ jobs:
defaults:
run:
- shell: bash -l {0}
+ shell: bash
steps:
- uses: actions/checkout@v6
- - name: Set up conda
- uses: conda-incubator/setup-miniconda@v3
+ - name: Install uv
+ uses: astral-sh/setup-uv@v8.3.2
with:
- miniforge-version: latest
- activate-environment: nwb-guide
- conda-remove-defaults: true
+ enable-cache: true
- - name: Create and activate environment
- run: conda env update --name nwb-guide --file environments/environment-Windows.yml
+ - name: Install Python dependencies
+ run: uv sync --locked
+
+ - name: Add the virtual environment to PATH
+ run: |
+ if [ "$RUNNER_OS" == "Windows" ]; then
+ echo "$GITHUB_WORKSPACE\\.venv\\Scripts" >> "$GITHUB_PATH"
+ else
+ echo "$GITHUB_WORKSPACE/.venv/bin" >> "$GITHUB_PATH"
+ fi
+ echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> "$GITHUB_ENV"
- uses: actions/setup-node@v6
with:
node-version: "20"
+ cache: 'npm'
- name: Install package.json modules and their dependencies
run: npm install --verbose
+ # Keep the released bundle consistent with the one exercised by the build tests.
+ # matplotlib arrives transitively through neuroconv's extras and GUIDE never imports it.
+ # PyInstaller bundles whatever is installed, and matplotlib's hidden libraries break the
+ # packaged build, so every job drops it to keep tests and releases on the same environment.
+ # `uv tree --invert --package matplotlib` lists what currently pulls it in.
+ - name: Manually remove matplotlib
+ run: uv pip uninstall matplotlib || true
+
- name: Build and deploy on Windows
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/testing_dev.yml b/.github/workflows/testing_dev.yml
index 9670e7abe..eadd7bdac 100644
--- a/.github/workflows/testing_dev.yml
+++ b/.github/workflows/testing_dev.yml
@@ -15,63 +15,54 @@ jobs:
runs-on: ${{ matrix.os }}
defaults:
run:
- shell: bash -l {0}
+ shell: bash
strategy:
fail-fast: false
matrix:
include:
- os: ubuntu-latest
- label: environments/environment-Linux.yml
- os: macos-latest # Mac arm64 runner
- label: environments/environment-MAC-apple-silicon.yml
- os: macos-15-intel # Mac x64 runner
- label: environments/environment-MAC-intel.yml
- os: windows-latest
- label: environments/environment-Windows.yml
steps:
- uses: actions/checkout@v6
- # see https://github.com/conda-incubator/setup-miniconda#caching-environments
- - name: Set up conda
- uses: conda-incubator/setup-miniconda@v3
+ - name: Install uv
+ uses: astral-sh/setup-uv@v8.3.2
with:
- miniforge-version: latest
- activate-environment: nwb-guide
- conda-remove-defaults: true
+ enable-cache: true
- - name: Set cache date
- id: get-date
- run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
- shell: bash
+ - name: Install Python dependencies
+ run: uv sync --locked
- - name: Cache Conda env
- uses: actions/cache@v5
- with:
- path: ${{ env.CONDA }}/envs
- key: conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
- id: cache
-
- - if: steps.cache.outputs.cache-hit != 'true'
- name: Create and activate environment
- run: conda env update --name nwb-guide --file ${{ matrix.label }}
+ - name: Add the virtual environment to PATH
+ run: |
+ if [ "$RUNNER_OS" == "Windows" ]; then
+ echo "$GITHUB_WORKSPACE\\.venv\\Scripts" >> "$GITHUB_PATH"
+ else
+ echo "$GITHUB_WORKSPACE/.venv/bin" >> "$GITHUB_PATH"
+ fi
+ echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> "$GITHUB_ENV"
- name: Use Node.js 20
uses: actions/setup-node@v6
with:
node-version: 20
+ cache: 'npm'
- name: Install GUIDE
run: npm ci --verbose
- - name: Install testing dependencies
- run: pip install pytest pytest-cov
-
+ # matplotlib arrives transitively through neuroconv's extras and GUIDE never imports it.
+ # PyInstaller bundles whatever is installed, and matplotlib's hidden libraries break the
+ # packaged build, so every job drops it to keep tests and releases on the same environment.
+ # `uv tree --invert --package matplotlib` lists what currently pulls it in.
- name: Manually remove matplotlib
- run: pip uninstall matplotlib --yes
+ run: uv pip uninstall matplotlib || true
- if: matrix.os != 'ubuntu-latest'
name: Run tests
diff --git a/.github/workflows/testing_dev_e2e_with_live_services.yml b/.github/workflows/testing_dev_e2e_with_live_services.yml
index f10853590..360b6b300 100644
--- a/.github/workflows/testing_dev_e2e_with_live_services.yml
+++ b/.github/workflows/testing_dev_e2e_with_live_services.yml
@@ -17,70 +17,71 @@ jobs:
runs-on: ${{ matrix.os }}
defaults:
run:
- shell: bash -l {0}
+ shell: bash
strategy:
fail-fast: false
matrix:
include:
- os: ubuntu-latest
- label: environments/environment-Linux.yml
- os: macos-latest # Mac arm64 runner
- label: environments/environment-MAC-apple-silicon.yml
- os: macos-15-intel # Mac x64 runner
- label: environments/environment-MAC-intel.yml
- os: windows-latest
- label: environments/environment-Windows.yml
steps:
- uses: actions/checkout@v6
- # see https://github.com/conda-incubator/setup-miniconda#caching-environments
- - name: Set up conda
- uses: conda-incubator/setup-miniconda@v3
+ - name: Install uv
+ uses: astral-sh/setup-uv@v8.3.2
with:
- miniforge-version: latest
- activate-environment: nwb-guide
- conda-remove-defaults: true
-
- - name: Set cache date
- id: get-date
- run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
- shell: bash
+ enable-cache: true
- - name: Cache Conda env
- uses: actions/cache@v5
- with:
- path: ${{ env.CONDA }}/envs
- key: conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
- id: cache
+ - name: Install Python dependencies
+ run: uv sync --locked
- - if: steps.cache.outputs.cache-hit != 'true'
- name: Create and activate environment
- run: conda env update --name nwb-guide --file ${{ matrix.label }}
+ - name: Add the virtual environment to PATH
+ run: |
+ if [ "$RUNNER_OS" == "Windows" ]; then
+ echo "$GITHUB_WORKSPACE\\.venv\\Scripts" >> "$GITHUB_PATH"
+ else
+ echo "$GITHUB_WORKSPACE/.venv/bin" >> "$GITHUB_PATH"
+ fi
+ echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> "$GITHUB_ENV"
- name: Use Node.js 20
uses: actions/setup-node@v6
with:
node-version: 20
+ cache: 'npm'
- name: Install GUIDE
run: npm ci --verbose
- - name: Install testing dependencies
- run: pip install pytest pytest-cov
-
+ # matplotlib arrives transitively through neuroconv's extras and GUIDE never imports it.
+ # PyInstaller bundles whatever is installed, and matplotlib's hidden libraries break the
+ # packaged build, so every job drops it to keep tests and releases on the same environment.
+ # `uv tree --invert --package matplotlib` lists what currently pulls it in.
- name: Manually remove matplotlib
- run: pip uninstall matplotlib --yes
+ run: uv pip uninstall matplotlib || true
- name: Create env file
run: |
touch .env
echo DANDI_SANDBOX_API_KEY=${{ secrets.DANDI_SANDBOX_API_KEY }} >> .env
- - if: matrix.os != 'ubuntu-latest'
+ # The macOS x64 runner intermittently crashes Chromium/Electron subprocesses (GPU and
+ # network-service), which fails the E2E run. Retry only on that runner.
+ - if: matrix.os == 'macos-15-intel'
+ name: Run tests (retried on the flaky x64 runner)
+ uses: nick-fields/retry@ad984534de44a9489a53aefd81eb77f87c70dc60 # v4.0.0
+ with:
+ timeout_minutes: 25
+ max_attempts: 5
+ command: npm run coverage:tutorial
+
+ - if: matrix.os == 'macos-latest' || matrix.os == 'windows-latest'
name: Run tests
run: npm run coverage:tutorial
diff --git a/.github/workflows/testing_dev_with_live_services.yml b/.github/workflows/testing_dev_with_live_services.yml
index b96de8774..ef0f512b8 100644
--- a/.github/workflows/testing_dev_with_live_services.yml
+++ b/.github/workflows/testing_dev_with_live_services.yml
@@ -15,64 +15,55 @@ jobs:
runs-on: ${{ matrix.os }}
defaults:
run:
- shell: bash -l {0}
+ shell: bash
strategy:
fail-fast: false
matrix:
include:
- os: ubuntu-latest
- label: environments/environment-Linux.yml
- os: macos-latest # Mac arm64 runner
- label: environments/environment-MAC-apple-silicon.yml
- os: macos-15-intel # Mac x64 runner
- label: environments/environment-MAC-intel.yml
- os: windows-latest
- label: environments/environment-Windows.yml
steps:
- uses: actions/checkout@v6
- # see https://github.com/conda-incubator/setup-miniconda#caching-environments
- - name: Set up conda
- uses: conda-incubator/setup-miniconda@v3
+ - name: Install uv
+ uses: astral-sh/setup-uv@v8.3.2
with:
- miniforge-version: latest
- activate-environment: nwb-guide
- conda-remove-defaults: true
+ enable-cache: true
- - name: Set cache date
- id: get-date
- run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
- shell: bash
+ - name: Install Python dependencies
+ run: uv sync --locked
- - name: Cache Conda env
- uses: actions/cache@v5
- with:
- path: ${{ env.CONDA }}/envs
- key: conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
- id: cache
-
- - if: steps.cache.outputs.cache-hit != 'true'
- name: Create and activate environment
- run: conda env update --name nwb-guide --file ${{ matrix.label }}
+ - name: Add the virtual environment to PATH
+ run: |
+ if [ "$RUNNER_OS" == "Windows" ]; then
+ echo "$GITHUB_WORKSPACE\\.venv\\Scripts" >> "$GITHUB_PATH"
+ else
+ echo "$GITHUB_WORKSPACE/.venv/bin" >> "$GITHUB_PATH"
+ fi
+ echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> "$GITHUB_ENV"
- name: Use Node.js 20
uses: actions/setup-node@v6
with:
node-version: 20
+ cache: 'npm'
- name: Install GUIDE
run: npm ci --verbose
- - name: Install testing dependencies
- run: pip install pytest pytest-cov
-
+ # matplotlib arrives transitively through neuroconv's extras and GUIDE never imports it.
+ # PyInstaller bundles whatever is installed, and matplotlib's hidden libraries break the
+ # packaged build, so every job drops it to keep tests and releases on the same environment.
+ # `uv tree --invert --package matplotlib` lists what currently pulls it in.
- name: Manually remove matplotlib
- run: pip uninstall matplotlib --yes
+ run: uv pip uninstall matplotlib || true
- if: matrix.os != 'ubuntu-latest'
name: Run tests
diff --git a/.github/workflows/testing_flask_build_and_dist.yml b/.github/workflows/testing_flask_build_and_dist.yml
index 940b19677..2312f2028 100644
--- a/.github/workflows/testing_flask_build_and_dist.yml
+++ b/.github/workflows/testing_flask_build_and_dist.yml
@@ -12,7 +12,7 @@ jobs:
runs-on: ${{ matrix.os }}
defaults:
run:
- shell: bash -l {0}
+ shell: bash
strategy:
fail-fast: false
matrix:
@@ -20,14 +20,11 @@ jobs:
# No linux in this matrix since installation instructions use dev mode instead of distributable
- os: macos-latest # Mac arm64 runner
- label: environments/environment-MAC-apple-silicon.yml
- os: macos-15-intel # Mac x64 runner
- label: environments/environment-MAC-intel.yml
- os: windows-latest
- label: environments/environment-Windows.yml
steps:
- uses: actions/checkout@v6
@@ -35,44 +32,38 @@ jobs:
- name: Printout architecture
run: uname -m
- # see https://github.com/conda-incubator/setup-miniconda#caching-environments
- - name: Set up conda
- uses: conda-incubator/setup-miniconda@v3
+ - name: Install uv
+ uses: astral-sh/setup-uv@v8.3.2
with:
- miniforge-version: latest
- activate-environment: nwb-guide
- conda-remove-defaults: true
+ enable-cache: true
- - name: Set cache date
- id: get-date
- run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
- shell: bash
+ - name: Install Python dependencies
+ run: uv sync --locked
- - name: Cache Conda env
- uses: actions/cache@v5
- with:
- path: ${{ env.CONDA }}/envs
- key:
- conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
- id: cache
-
- - if: steps.cache.outputs.cache-hit != 'true'
- name: Update environment
- run: conda env update --name nwb-guide --file ${{ matrix.label }}
+ - name: Add the virtual environment to PATH
+ run: |
+ if [ "$RUNNER_OS" == "Windows" ]; then
+ echo "$GITHUB_WORKSPACE\\.venv\\Scripts" >> "$GITHUB_PATH"
+ else
+ echo "$GITHUB_WORKSPACE/.venv/bin" >> "$GITHUB_PATH"
+ fi
+ echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> "$GITHUB_ENV"
- name: Setup Node.js 20
uses: actions/setup-node@v6
with:
node-version: "20"
+ cache: 'npm'
- name: Install GUIDE
run: npm ci --verbose
- - name: Install testing dependencies
- run: pip install pytest pytest-cov
-
+ # matplotlib arrives transitively through neuroconv's extras and GUIDE never imports it.
+ # PyInstaller bundles whatever is installed, and matplotlib's hidden libraries break the
+ # packaged build, so every job drops it to keep tests and releases on the same environment.
+ # `uv tree --invert --package matplotlib` lists what currently pulls it in.
- name: Manually remove matplotlib
- run: pip uninstall matplotlib --yes
+ run: uv pip uninstall matplotlib || true
- name: Build PyFlask distribution
run: npm run build:flask
diff --git a/.github/workflows/testing_pipelines.yml b/.github/workflows/testing_pipelines.yml
index f35ab4290..89676297c 100644
--- a/.github/workflows/testing_pipelines.yml
+++ b/.github/workflows/testing_pipelines.yml
@@ -12,63 +12,55 @@ jobs:
runs-on: ${{ matrix.os }}
defaults:
run:
- shell: bash -l {0}
+ shell: bash
strategy:
fail-fast: false
matrix:
include:
# Fails randomly on daily tests
# - os: ubuntu-latest
-# label: environments/environment-Linux.yml
- os: macos-latest # Mac arm64 runner
- label: environments/environment-MAC-apple-silicon.yml
- os: macos-15-intel # Mac x64 runner
- label: environments/environment-MAC-intel.yml
- os: windows-latest
- label: environments/environment-Windows.yml
steps:
- uses: actions/checkout@v6
- # see https://github.com/conda-incubator/setup-miniconda#caching-environments
- - name: Set up conda
- uses: conda-incubator/setup-miniconda@v3
- with:
- miniforge-version: latest
- activate-environment: nwb-guide
- conda-remove-defaults: true
-
- # Setup conda environment from cache
- - name: Set environment cache date
- id: get-date
- run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
- shell: bash
- - name: Cache Conda env
- uses: actions/cache@v5
+ - name: Install uv
+ uses: astral-sh/setup-uv@v8.3.2
with:
- path: ${{ env.CONDA }}/envs
- key: conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
- id: cache
- - if: steps.cache.outputs.cache-hit != 'true'
- name: Create and activate environment
- run: conda env update --name nwb-guide --file ${{ matrix.label }}
+ enable-cache: true
+
+ - name: Install Python dependencies
+ run: uv sync --locked
+
+ - name: Add the virtual environment to PATH
+ run: |
+ if [ "$RUNNER_OS" == "Windows" ]; then
+ echo "$GITHUB_WORKSPACE\\.venv\\Scripts" >> "$GITHUB_PATH"
+ else
+ echo "$GITHUB_WORKSPACE/.venv/bin" >> "$GITHUB_PATH"
+ fi
+ echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> "$GITHUB_ENV"
- name: Use Node.js 20
uses: actions/setup-node@v6
with:
node-version: 20
+ cache: 'npm'
- name: Install GUIDE
run: npm ci --verbose
- - name: Install testing dependencies
- run: pip install pytest pytest-cov
-
+ # matplotlib arrives transitively through neuroconv's extras and GUIDE never imports it.
+ # PyInstaller bundles whatever is installed, and matplotlib's hidden libraries break the
+ # packaged build, so every job drops it to keep tests and releases on the same environment.
+ # `uv tree --invert --package matplotlib` lists what currently pulls it in.
- name: Manually remove matplotlib
- run: pip uninstall matplotlib --yes
+ run: uv pip uninstall matplotlib || true
# Load example data caches
- name: Get ephy_testing_data current head hash
diff --git a/.gitignore b/.gitignore
index f205099de..8bbee71a8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,6 +22,8 @@ build/
yarn.lock
*.pyc
+.venv/
+*.egg-info/
.DS_Store
electron-builder.yml
website/.eslintcache
diff --git a/.python-version b/.python-version
new file mode 100644
index 000000000..f3fe474ae
--- /dev/null
+++ b/.python-version
@@ -0,0 +1 @@
+3.12.9
diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst
index 70610a7d2..4db831a55 100644
--- a/docs/developer_guide.rst
+++ b/docs/developer_guide.rst
@@ -24,76 +24,35 @@ Start by cloning the repository
Install Python Dependencies
^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Install the appropriate Python dependencies for your operating system.
+NWB GUIDE uses `uv `_ to manage its Python environment. Install ``uv`` by following the `uv installation instructions `_.
-**Windows**
+From the root of the repository, create the Python environment. ``uv`` reads the pinned Python version from ``.python-version`` (downloading it if necessary) and installs the locked dependencies into a ``.venv`` directory.
.. code-block:: bash
- conda env create --file ./environments/environment-Windows.yml
-
-**Mac with x64 architecture**
-
-.. code-block:: bash
-
- conda env create --file ./environments/environment-MAC-intel.yml
-
-**Mac with arm64 architecture**
-
-.. code-block:: bash
-
- conda env create --file ./environments/environment-MAC-apple-silicon.yml
-
-**Linux**
-
-.. code-block:: bash
-
- conda env create --file ./environments/environment-Linux.yml
-
-
-.. note::
-
- The NWB GUIDE environment can be quite large. If your base folder for ``conda`` is on a small mounted partition, you may need to setup the environment elsewhere on your system. You can do this using:
-
- .. code-block:: bash
-
- conda env create --file ./environments/environment-< platform >.yml --prefix < explicit location to setup environment >
-
- For example, on a remote Linux server, this might look like:
-
- .. code-block:: bash
-
- conda env create --file ./environments/environment-Linux.yml --prefix /mnt/data/nwb-guide
+ uv sync
Activate the Python Environment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Before starting NWB GUIDE, you'll need to ensure that the Python environment is activated.
+Before starting NWB GUIDE, activate the environment so that ``python`` resolves to the project interpreter.
.. code-block:: bash
- conda activate nwb-guide
+ source .venv/bin/activate
-.. note::
-
- If you had to use the ``--prefix`` flag in the previous step, then this becomes
-
- .. code-block:: bash
+On Windows, activate the environment instead with:
- conda activate < explicit location of environment >
-
- Such as, using the previous example:
-
- .. code-block:: bash
+.. code-block:: bash
- conda activate /mnt/data/nwb-guide
+ .venv\Scripts\activate
Install JavaScript Dependencies
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Next, install all JavaScript dependencies based on the `package-lock.json` file.
+NWB GUIDE requires `Node.js `_ 18 or later. After installing Node.js, install all JavaScript dependencies based on the ``package-lock.json`` file.
.. code-block:: bash
diff --git a/environments/environment-Linux.yml b/environments/environment-Linux.yml
deleted file mode 100644
index 0223c02dd..000000000
--- a/environments/environment-Linux.yml
+++ /dev/null
@@ -1,28 +0,0 @@
-name: nwb-guide
-channels:
- - conda-forge
- - defaults
-dependencies:
- - python = 3.12.9
- - nodejs = 18.16.1
- # install these from conda-forge so that dependent packages get included in the distributable
- - jsonschema = 4.18.0 # installs jsonschema-specifications
- - pip
- - pip:
- - chardet == 5.1.0
- - configparser == 6.0.0
- - flask == 2.3.2
- - flask-cors == 4.0.0
- - flask_restx == 1.1.0
- - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
- - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.9.3
- - spikeinterface >= 0.104.8 # ecephys backend (transitive dependency of neuroconv); 0.104.8+ supports ignore_low_freq_error used by tutorial data generation
- - scipy >= 1.18.0 # transitive dependency; nwb-guide.spec bundles scipy._external.array_api_compat.numpy.fft, which moved to that path in scipy 1.18.0
- - pandas < 3 # pandas 3.0 makes DataFrame.values read-only (copy-on-write), which breaks spikeinterface's in-place Phy unit_id assignment
- - scikit-learn == 1.6.1 # Tutorial data generation
- - tqdm_publisher == 0.1.1 # Progress bars
- - tzlocal == 5.3.1 # Frontend timezone handling
- - ndx-pose == 0.2.2
- - nwbinspector == 0.6.5
- - tables
- - numcodecs == 0.15.1 # numcodecs 0.16.0 is not compatible with zarr 2.18.5
diff --git a/environments/environment-MAC-apple-silicon.yml b/environments/environment-MAC-apple-silicon.yml
deleted file mode 100644
index af59d6250..000000000
--- a/environments/environment-MAC-apple-silicon.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-name: nwb-guide
-channels:
- - conda-forge
- - defaults
-dependencies:
- - python = 3.12.9
- - nodejs = 18.16.1
- # Install these from conda-forge so that dependent packages get included in the distributable
- - lxml = 4.9.3 # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
- - pyedflib = 0.1.38 # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
- - numpy # May have x64/arm64 mismatch issues so install from conda-forge
- - pytables = 3.10.2 # PyPI build fails on arm64 so install from conda-forge (used by neuroconv deps)
- - jsonschema = 4.18.0 # Also installs jsonschema-specifications
- - pip
- - pip:
- - setuptools==70.0.0
- - PyInstaller==6.14.2
- - chardet == 5.1.0
- - configparser == 6.0.0
- - flask == 2.3.2
- - flask-cors == 4.0.0
- - flask_restx == 1.1.0
- - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
- - h5py < 3.13 # 3.13+ uses HDF5 1.14.4 features not in pytables 3.10.2's bundled HDF5 1.14.2
- - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.9.3
- - spikeinterface >= 0.104.8 # ecephys backend (transitive dependency of neuroconv); 0.104.8+ supports ignore_low_freq_error used by tutorial data generation
- - scipy >= 1.18.0 # transitive dependency; nwb-guide.spec bundles scipy._external.array_api_compat.numpy.fft, which moved to that path in scipy 1.18.0
- - pandas < 3 # pandas 3.0 makes DataFrame.values read-only (copy-on-write), which breaks spikeinterface's in-place Phy unit_id assignment
- - scikit-learn == 1.6.1 # Tutorial data generation
- - tqdm_publisher == 0.1.1 # Progress bars
- - tzlocal == 5.3.1 # Frontend timezone handling
- - ndx-pose == 0.2.2
- - nwbinspector == 0.6.5
- - numcodecs == 0.15.1 # numcodecs 0.16.0 is not compatible with zarr 2.18.5
diff --git a/environments/environment-MAC-intel.yml b/environments/environment-MAC-intel.yml
deleted file mode 100644
index cbdd1f8f1..000000000
--- a/environments/environment-MAC-intel.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: nwb-guide
-channels:
- - conda-forge
- - defaults
-dependencies:
- - python = 3.12.9
- - nodejs = 18.16.1
- # install these from conda-forge so that dependent packages get included in the distributable
- - jsonschema = 4.18.0 # installs jsonschema-specifications
- - pip
- - pip:
- - setuptools==70.0.0
- - PyInstaller==6.14.2
- - chardet == 5.1.0
- - configparser == 6.0.0
- - flask == 2.3.2
- - flask-cors == 4.0.0
- - flask_restx == 1.1.0
- - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
- - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.9.3
- - spikeinterface >= 0.104.8 # ecephys backend (transitive dependency of neuroconv); 0.104.8+ supports ignore_low_freq_error used by tutorial data generation
- - scipy >= 1.18.0 # transitive dependency; nwb-guide.spec bundles scipy._external.array_api_compat.numpy.fft, which moved to that path in scipy 1.18.0
- - pandas < 3 # pandas 3.0 makes DataFrame.values read-only (copy-on-write), which breaks spikeinterface's in-place Phy unit_id assignment
- - scikit-learn == 1.6.1 # Tutorial data generation
- - tqdm_publisher == 0.1.1 # Progress bars
- - tzlocal == 5.3.1 # Frontend timezone handling
- - ndx-pose == 0.2.2
- - nwbinspector == 0.6.5
- - numcodecs == 0.15.1 # numcodecs 0.16.0 is not compatible with zarr 2.18.5
- - h5py == 3.12.1 # 3.13.0 uses features in hdf5 1.14.4 that is not available in earlier hdf5 libs packaged
- # with tables==3.9.1 (latest that can be used by neuroconv 0.6.0).
- # h5py and tables need to be consistent for electron build for unknown reason
- - ruamel.yaml.clib != 0.2.13 # 0.2.13 throws a build error on intel Mac -- see https://github.com/catalystneuro/roiextractors/issues/489
diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml
deleted file mode 100644
index faf70f76b..000000000
--- a/environments/environment-Windows.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-name: nwb-guide
-channels:
- - defaults
- - conda-forge
-dependencies:
- - python = 3.12.9
- - nodejs = 18.16.1
- - pywin32 = 308
- - git = 2.20.1
- - pip
- - pip:
- - setuptools==70.0.0
- - PyInstaller==6.14.2
- - chardet == 5.1.0
- - configparser == 6.0.0
- - flask == 2.3.2
- - flask-cors === 3.0.10
- - flask_restx == 1.1.0
- - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
- - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.9.3
- - spikeinterface >= 0.104.8 # ecephys backend (transitive dependency of neuroconv); 0.104.8+ supports ignore_low_freq_error used by tutorial data generation
- - scipy >= 1.18.0 # transitive dependency; nwb-guide.spec bundles scipy._external.array_api_compat.numpy.fft, which moved to that path in scipy 1.18.0
- - pandas < 3 # pandas 3.0 makes DataFrame.values read-only (copy-on-write), which breaks spikeinterface's in-place Phy unit_id assignment
- - scikit-learn == 1.6.1 # Tutorial data generation
- - tqdm_publisher == 0.1.1 # Progress bars
- - tzlocal == 5.3.1 # Frontend timezone handling
- - ndx-pose == 0.2.2
- - nwbinspector == 0.6.5
- - tables
- - numcodecs == 0.15.1 # numcodecs 0.16.0 is not compatible with zarr 2.18.5
diff --git a/pyproject.toml b/pyproject.toml
index 05c6c9875..472128830 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,55 @@
+[project]
+name = "nwb-guide"
+# The authoritative version lives in package.json; this project is never built or published.
+dynamic = ["version"]
+description = "NWB GUIDE is a desktop app that provides a no-code user interface for converting neurophysiology data to NWB."
+readme = "README.md"
+license = { text = "MIT" }
+authors = [{ name = "CatalystNeuro" }]
+requires-python = ">=3.12,<3.13"
+dependencies = [
+ "chardet==5.1.0",
+ "configparser==6.0.0",
+ "flask==2.3.2",
+ "flask-cors==4.0.0",
+ "flask-restx==1.1.0",
+ "werkzeug<3.0", # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
+ "h5py<3.13", # keep the HDF5 version aligned with the pytables build for a working PyInstaller bundle
+ "jsonschema==4.18.0", # also installs jsonschema-specifications
+ "neuroconv[dandi,compressors,ecephys,ophys,behavior,text]==0.9.3",
+ "scikit-learn==1.6.1", # tutorial data generation
+ "tqdm-publisher==0.1.1", # progress bars
+ "tzlocal==5.3.1", # frontend timezone handling
+ "ndx-pose==0.2.2",
+ "nwbinspector==0.6.5",
+ "numcodecs==0.15.1", # numcodecs 0.16.0 is not compatible with zarr 2.18.5
+ "setuptools==70.0.0", # provides pkg_resources for bundled dependencies
+ "pywin32==308; sys_platform == 'win32'",
+]
+
+[dependency-groups]
+dev = [
+ "pyinstaller==6.14.2", # builds the standalone backend distributable
+ "pytest",
+ "pytest-cov",
+]
+
+[tool.uv]
+package = false
+# Constraints apply only to transitive dependencies that another package already pulls in.
+constraint-dependencies = [
+ # ruamel.yaml.clib 0.2.13 fails to build on Intel macOS.
+ # https://github.com/catalystneuro/roiextractors/issues/489
+ "ruamel.yaml.clib!=0.2.13",
+ # Tutorial data generation passes ignore_low_freq_error to bandpass_filter, added in 0.104.8.
+ "spikeinterface>=0.104.8",
+ # nwb-guide.spec bundles scipy._external.array_api_compat.numpy.fft, which moved there in scipy 1.18.0.
+ "scipy>=1.18.0",
+ # pandas 3.0 makes DataFrame.values read-only (copy-on-write), which breaks spikeinterface's
+ # in-place Phy unit_id assignment. https://github.com/SpikeInterface/spikeinterface/issues/4687
+ "pandas<3",
+]
+
[tool.black]
line-length = 120
target-version = ['py37']
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 000000000..b581d4286
--- /dev/null
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@@ -0,0 +1,3085 @@
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