From 1c1659b7874abe20d322810b09f81d655da0c230 Mon Sep 17 00:00:00 2001 From: willGraham01 <1willgraham@gmail.com> Date: Wed, 3 Jan 2024 14:34:39 +0000 Subject: [PATCH 1/6] Reinstate brainmapper CLI check --- .github/workflows/test_and_deploy.yml | 57 +++++++++++++-------------- 1 file changed, 28 insertions(+), 29 deletions(-) diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index fb74cb66..3a71fd36 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -92,43 +92,42 @@ jobs: # Run brainglobe-workflows brainmapper-CLI tests to check for # breakages - # test_brainmapper_cli: - # needs: [linting, manifest] - # name: Run brainmapper tests to check for breakages - # runs-on: ubuntu-latest - # steps: - # - name: Cache tensorflow model - # uses: actions/cache@v3 - # with: - # path: "~/.cellfinder" - # key: models-${{ hashFiles('~/.cellfinder/**') }} + test_brainmapper_cli: + needs: [linting, manifest] + name: Run brainmapper tests to check for breakages + runs-on: ubuntu-latest + steps: + - name: Cache tensorflow model + uses: actions/cache@v3 + with: + path: "~/.cellfinder" + key: models-${{ hashFiles('~/.cellfinder/**') }} - # - name: Checkout brainglobe-workflows - # uses: actions/checkout@v3 - # with: - # repository: 'brainglobe/brainglobe-workflows' + - name: Checkout brainglobe-workflows + uses: actions/checkout@v3 + with: + repository: 'brainglobe/brainglobe-workflows' - # - name: Set up Python 3.10 - # uses: actions/setup-python@v3 - # with: - # python-version: "3.10" + - name: Set up Python 3.10 + uses: actions/setup-python@v3 + with: + python-version: "3.10" - # - name: Install test dependencies - # run: | - # python -m pip install --upgrade pip wheel - # # Install latest SHA on this brainglobe-workflows branch - # python -m pip install git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA - # # Install checked out copy of brainglobe-workflows - # python -m pip install .[dev] + - name: Install test dependencies + run: | + python -m pip install --upgrade pip wheel + # Install latest SHA on this brainglobe-workflows branch + python -m pip install git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA + # Install checked out copy of brainglobe-workflows + python -m pip install .[dev] - # - name: Run brainmapper tests in brainglobe-workflows - # run: | - # python -m pytest --color=yes -v tests/brainmapper + - name: Run brainmapper tests in brainglobe-workflows + run: | + python -m pytest --color=yes -v tests/brainmapper build_sdist_wheel: name: Build source distribution and wheel # needs: [test, test_brainmapper_cli, test_numba_disabled] - needs: [test] if: github.event_name == 'push' && github.ref_type == 'tag' runs-on: ubuntu-latest steps: From 62c7cba2d540f9b553d75928d273e003cf5cfd0f Mon Sep 17 00:00:00 2001 From: willGraham01 <1willgraham@gmail.com> Date: Wed, 3 Jan 2024 11:39:57 +0000 Subject: [PATCH 2/6] Update README to point to brainmapper pages --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index eebfa5e7..82b0e4c4 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ For more details, head over to [the documentation website](https://brainglobe.in At a glance: -- There is a [command-line interface](https://brainglobe.info/documentation/cellfinder/user-guide/command-line/index.html) that integrates [with `brainreg`](https://github.com/brainglobe/brainreg) for automated cell detection and classification. +- There is a command-line interface called [brainmapper](https://brainglobe.info/documentation/brainglobe-workflows/brainmapper/index.html) that integrates [with `brainreg`](https://github.com/brainglobe/brainreg) for automated cell detection and classification. You can install it through [`brainglobe-workflows`](https://brainglobe.info/documentation/brainglobe-workflows/index.html). - There is a [napari plugin](https://brainglobe.info/documentation/cellfinder/user-guide/napari-plugin/index.html) for interacting graphically with the cellfinder tool. - There is a [Python API](https://brainglobe.info/documentation/cellfinder/user-guide/cellfinder-core.html) to allow users to integrate BrainGlobe tools into their custom workflows. From 98e138890f9439daf0fa0dbc12e5fdc6f7511b33 Mon Sep 17 00:00:00 2001 From: willGraham01 <1willgraham@gmail.com> Date: Wed, 3 Jan 2024 11:45:17 +0000 Subject: [PATCH 3/6] Update install instructions --- README.md | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 82b0e4c4..3f65584c 100644 --- a/README.md +++ b/README.md @@ -26,14 +26,24 @@ At a glance: ## Installation You can find [the installation instructions](https://brainglobe.info/documentation/cellfinder/installation.html#installation) on the BrainGlobe website, which will go into more detail about the installation process if you want to minimise your installation to suit your needs. -However, we recommend that users install `cellfinder` either through installing BrainGlobe version 1, or (if you also want the command-line interface) installing `brainglobe-workflows`: +However, we recommend that users install `cellfinder` either through installing BrainGlobe version 1, or (if you also want the command-line interface) installing `brainglobe-workflows`. ```bash -pip install cellfinder>=1.0.0 # If you just want the napari plugin and Python API -pip install brainglobe>=1.0.0 # If you want to install all BrainGlobe tools, including cellfinder, in a consistent manner with one command -pip install brainglobe-workflows>=1.0.0 # If you want to include the CLI +# If you want to install all BrainGlobe tools, including cellfinder, in a consistent manner with one command: +pip install brainglobe>=1.0.0 +# If you want to install the brainmapper CLI tool as well: +pip install brainglobe-workflows>=1.0.0 ``` +If you only want the `cellfinder` package by itself, you can `pip install` it alone: + +```bash +pip install cellfinder>=1.0.0 +``` + +Be sure to specify a version greater than version `v1.0.0` - prior to this version the `cellfinder` package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite. +See [our blog posts](https://brainglobe.info/blog/) for more information on the release of BrainGlobe version 1. + ## Contributing If you have encountered a bug whilst using cellfinder, please [open an issue on GitHub](https://github.com/brainglobe/cellfinder/issues). From dcb9b19fced82d4efb3bd4be8099b556c1eda196 Mon Sep 17 00:00:00 2001 From: willGraham01 <1willgraham@gmail.com> Date: Wed, 3 Jan 2024 14:33:12 +0000 Subject: [PATCH 4/6] Drop python 3.8 support --- .github/workflows/test_and_deploy.yml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 3a71fd36..77d09db0 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -40,7 +40,7 @@ jobs: matrix: # Run all supported Python versions on linux os: [ubuntu-latest] - python-version: ["3.8", "3.9", "3.10"] + python-version: ["3.9", "3.10"] # Include one windows, one macos run include: - os: macos-latest diff --git a/pyproject.toml b/pyproject.toml index 3b531deb..2e2231b0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ classifiers = [ "Programming Language :: Python :: 3.10", "Topic :: Scientific/Engineering :: Image Recognition", ] -requires-python = ">=3.8" +requires-python = ">=3.9" dependencies = [ "brainglobe-utils", "dask[array]", From 2b620d6f9c75f292b1838420bc56f7ec241745b7 Mon Sep 17 00:00:00 2001 From: willGraham01 <1willgraham@gmail.com> Date: Wed, 3 Jan 2024 14:35:24 +0000 Subject: [PATCH 5/6] Fix rebase barfs --- .github/workflows/test_and_deploy.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 77d09db0..e620eb5b 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -127,7 +127,7 @@ jobs: build_sdist_wheel: name: Build source distribution and wheel - # needs: [test, test_brainmapper_cli, test_numba_disabled] + needs: [test, test_brainmapper_cli, test_numba_disabled] if: github.event_name == 'push' && github.ref_type == 'tag' runs-on: ubuntu-latest steps: From 6aafafa8ff541d92d7bab8e6186fbc346fc61086 Mon Sep 17 00:00:00 2001 From: willGraham01 <1willgraham@gmail.com> Date: Wed, 3 Jan 2024 14:46:25 +0000 Subject: [PATCH 6/6] pre-commit pass --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3f65584c..ef352760 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,7 @@ However, we recommend that users install `cellfinder` either through installing ```bash # If you want to install all BrainGlobe tools, including cellfinder, in a consistent manner with one command: -pip install brainglobe>=1.0.0 +pip install brainglobe>=1.0.0 # If you want to install the brainmapper CLI tool as well: pip install brainglobe-workflows>=1.0.0 ```