Make Mayavi optional

docs/install.md

@@ -12,7 +12,7 @@
 
 ## Installation Options
 
-MagellanMapper can be installed depending on one's Python preferences.
+MagellanMapper supports several Python setups.
 
 ### Install using Conda
 
@@ -41,27 +41,28 @@ Install using Pip with Python >= 3.6 (see [Python versions](#python-version-supp
 pip install magellanmapper[most] --extra-index-url https://pypi.fury.io/dd8/
 ```
 
-The `most` group installs the GUI and file import tools. The extra index accesses a few [customized dependencies](#custom-packages) for MagellanMapper.
+The `most` group installs the GUI and file import tools (see [optional dependencies below](#optional-installation-groups)). The extra index accesses a few [customized dependencies](#custom-packages) for MagellanMapper.
 
 Java will need to be installed to support more image formats (eg from [here](https://www.azul.com/downloads/?package=jdk)).
 
 ### Developer installs
 
-If you download the source code, you can install in developer mode for the latest updates and any changes you make.
+You can install directly from the source code for the latest updates.
 
-Download the repo:
+First, download the repo:
 
 ```shell
 git clone https://github.com/sanderslab/magellanmapper.git
 ```
 
-For Conda:
+Next, install it:
+- For Conda:
 
 ```shell
 conda env create -n mag -f environment.yml
 ```
 
-Or Pip:
+- Or Pip:
 
 ```shell
 pip install -e .[most] --extra-index-url https://pypi.fury.io/dd8/
@@ -152,7 +153,7 @@ On Windows, the [Microsoft Visual C++ Redistributable for Visual Studio 2015, 20
 If installed from a Python package, enter your virtual environment and run:
 
 ```shell
-pip install -U magellanmapper  --extra-index-url https://pypi.fury.io/dd8/
+pip install -U magellanmapper --extra-index-url https://pypi.fury.io/dd8/
 ```
 
 If installed from source:
@@ -167,27 +168,15 @@ Sometimes a virtual environment update is required for new depdendencies.
 
 ## Dependencies
 
-The main required and optional dependencies in MagellanMapper are:
-
-- Scipy, Numpy, Matplotlib stack
-- Mayavi/TraitsUI/Qt stack for GUI and 3D visualization
-- Scikit-image for image processing
-- Scikit-learn for machine learning based stats
-- Pandas for stats
-- [SimpleElastix](https://github.com/SuperElastix/SimpleElastix), a fork of SimpleITK with Elastix integrated (see below)
-- Python-Bioformats/Javabridge for importing images from propriety formast such as `.czi` (optional, requires Java SDK and C compiler)
-
 ### Python version support
 
 | MagellanMapper Version | Python Versions Supported | Deprecations |
 |-----|-----|-----|
 | < 1.4 | 3.6 | None |
 | 1.4-1.5 | 3.6-3.9 (no GUI support in 3.9) | None |
-| 1.6a1-a2 | 3.6-3.9 (GUI support added for 3.9; MM 1.6a2 base group no longer installs GUI) | 3.6-3.7 to be removed in MM 1.7 |
+| 1.6a1-a3 | 3.6-3.9 (GUI support added for 3.9; MM 1.6a2 base group no longer installs GUI) | 3.6-3.7 to be removed in MM 1.7 |
 | 1.6b1 | 3.6-3.11 (no GUI support in 3.10-3.11 as of 2022-12-30) | Same |
 
-The `bin/setup_multi_venvs.sh`, `bin/build_deps.sh`, and their `.bat` counterparts are provided to build these dependencies for multiple Python versions.
-
 As of MM 1.6a2, the GUI can be excluded by installing the base group, eg without `[gui]` or `[most]`.
 
 ### Pinned packages
@@ -199,6 +188,21 @@ We've provided a few sets of pinned dependency versions:
 
 These package versions are used for automated testing (continuous integration).
 
+### Optional installation groups
+
+| Group | Packages | Collection |
+|-----|-----|-----|
+| `most` | Import and GUI tools | Has `import`, `gui` |
+| `all` | All groups plus `seaborn`, `scikit-learn` | Has all below |
+| `import` | Imports proprietary image formats | |
+| `gui` | Main graphical interface | |
+| `pandas_plus` | Exports styled and Excel formats | |
+| `aws` | Tools for accessing AWS | |
+| `docs` | Tools for building docs | |
+| `jupyter` | Running Notebooks | |
+| `classifer` | Tensorflow | |
+| `3D` | 3D rendering | |
+
 ### Optional Dependency Build and Runtime Requirements
 
 #### Custom packages
@@ -418,6 +422,12 @@ Additional errors:
 
 - An error with VTK has prevented display of 3D images at least as of VTK 8.1.2 on RHEL 7.5, though the same VTK version works on Ubuntu 18.04
 
+```Building TVTK classes... Windows fatal exception: code 0xc0000374``` or ```Building TVTK classes... Fatal Python error: Segmentation fault```
+
+* Appears to be a sporadic installation issue (see [issue](https://github.com/sanderslab/magellanmapper/issues/401))
+* Workaround: reinstall Mayavi: `pip install mayavi`
+* Starting with MM v1.6a4, Mayavi will no longer be installed by defaul
+
 ### Display issues
 
 #### Window is too large for screen

docs/release/release_v1.6.md

@@ -6,6 +6,7 @@
 
 - Smoother, faster interactions with main plots, including atlas label name display, label editing, and pan and zoom navigation
 - Available as binary wheel to install without requiring the source code
+- Faster, lighter installation with fewer required dependency packages
 - Simpler entry point to launch MagellanMapper: `mm`
 - Atlases can be downloaded directly through [`BrainGlobe`](https://github.com/brainglobe/bg-atlasapi) (see the new "Atlases" panel)
 - Atlas regions can be searched (see "Atlases > Region")
@@ -177,7 +178,8 @@
 - Updated to use the `axis_channel` parameter in Scikit-image's `transform.rescale` function (#115)
 - Seaborn as an optional dependency for additional plot support (currently only swarm plots, #137)
 - Scikit-learn is an optional rather than a required dependency (#150)
-- The AWS-related dependencies (`boto3`, `awscli`) are now optional (#150, #379)
+- The AWS-related dependencies (`boto3`, `awscli`) are now optional, installed in the `aws` group (#150, #379)
+- Mayavi/VTK are now optional, installed in the `3d` group (#455)
 - The `jupyter` install group installs packages for running the Jupyter sample commands notebook in a Bash kernel (#122)
 - Missing dependencies are starting to use more consistent error messages and instructions (#226)
 - Python 3.6 and 3.7 have been deprecated for removal in MM v1.7 and have separate pinned dependencies (`envs/requirements_py3<n>`) (#232, #379)

envs/requirements.txt

@@ -1,56 +1,53 @@
 --extra-index-url https://pypi.fury.io/dd8/
 appdirs==1.4.4
-apptools==5.2.0
 bg-atlasapi @ https://github.com/brainglobe/bg-atlasapi/archive/dbecd16b2f63a8e167543f3358452a756bad0e64.tar.gz
 bg-space==0.6.0
 certifi==2022.12.7
-charset-normalizer==2.1.1
+charset-normalizer==3.0.1
 click==8.1.3
-commonmark==0.9.1
-configobj==5.0.6
-contourpy==1.0.6
+contourpy==1.0.7
 cycler==0.11.0
-envisage==6.1.0
 fonttools==4.38.0
 future==0.18.3
 idna==3.4
-imagecodecs==2022.12.24
-imageio==2.23.0
-importlib-resources==5.10.2
+imagecodecs==2023.1.23
+imageio==2.26.0
+importlib-resources==5.12.0
 javabridge==1.0.19.post9+gc8c12b4
 kiwisolver==1.4.4
-matplotlib==3.6.2
+lazy_loader==0.1
+markdown-it-py==2.2.0
+matplotlib==3.7.0
 matplotlib-scalebar==0.8.1
-mayavi==4.8.1
+mdurl==0.1.2
 meshio==5.3.4
-networkx==2.8.8
+networkx==3.0
 numpy==1.24.2
-packaging==22.0
+packaging==23.0
 pandas==1.5.3
 Pillow==9.4.0
 pyamg==4.2.3
 pyface==7.4.4
 Pygments==2.14.0
 pyparsing==3.0.9
-PyQt5==5.15.7
+PyQt5==5.15.9
 PyQt5-Qt5==5.15.2
-PyQt5-sip==12.11.0
+PyQt5-sip==12.11.1
 python-bioformats==4.0.7.post5+g52309d1
 python-dateutil==2.8.2
-pytz==2022.7
+pytz==2022.7.1
 PyWavelets==1.4.1
 PyYAML==6.0
-requests==2.28.1
-rich==13.0.0
-scikit-image==0.19.3
-scipy==1.10.0
+requests==2.28.2
+rich==13.3.1
+scikit-image==0.20.0
+scipy==1.9.1
 SimpleITK==2.3.0.dev117+g0640d
 six==1.16.0
-tifffile==2022.10.10
+tifffile==2023.2.28
 traits==6.4.1
-traitsui==7.4.2
+traitsui==7.4.3
 treelib==1.6.1
-typing_extensions==4.4.0
-urllib3==1.26.13
-vtk==9.2.4
-zipp==3.11.0
+typing_extensions==4.5.0
+urllib3==1.26.14
+zipp==3.15.0

envs/requirements_py36

@@ -1,28 +1,19 @@
 --extra-index-url https://pypi.fury.io/dd8/
-aiohttp==3.8.1
-aiosignal==1.2.0
 appdirs==1.4.4
-apptools==5.1.0
-async-timeout==4.0.2
-asynctest==0.13.0
-attrs==21.4.0
 bg-atlasapi @ https://github.com/brainglobe/bg-atlasapi/archive/dbecd16b2f63a8e167543f3358452a756bad0e64.tar.gz
 bg-space==0.6.0
 boto3==1.23.10
 botocore==1.26.10
-certifi==2022.6.15
+certifi==2022.12.7
 charset-normalizer==2.0.12
 click==8.0.4
 commonmark==0.9.1
-configobj==5.0.6
 cycler==0.11.0
-dataclasses==0.8;python_version<"3.7"
+dataclasses==0.8
 decorator==4.4.2
-envisage==6.0.1
-frozenlist==1.2.0
-future==0.18.2
-idna==3.3
-idna-ssl==1.1.0
+future==0.18.3
+idna==3.4
+imagecodecs==2020.5.30
 imageio==2.15.0
 importlib-metadata==4.8.3
 importlib-resources==5.4.0
@@ -31,40 +22,34 @@ jmespath==0.10.0
 kiwisolver==1.3.1
 matplotlib==3.3.4
 matplotlib-scalebar==0.7.2
-mayavi==4.8.0
 meshio==4.4.6
-multidict==5.2.0
 networkx==2.5.1
 numpy==1.19.5
 pandas==1.1.5
 Pillow==8.4.0
 pyamg==4.2.3
-pyface==7.4.2
-Pygments==2.12.0
+pyface==7.4.4
+Pygments==2.14.0
 pyparsing==3.0.9
 PyQt5==5.15.6
 PyQt5-Qt5==5.15.2
 PyQt5-sip==12.9.1
 python-bioformats==4.0.5.post2+g51eb88a
 python-dateutil==2.8.2
-pytz==2022.1
+pytz==2022.7.1
 PyWavelets==1.1.1
 PyYAML==6.0
 requests==2.27.1
-rich==12.5.1
+rich==12.6.0
 s3transfer==0.5.2
-scikit-image==0.17.2;python_version<"3.9"
-scikit-image==0.19.3;python_version>="3.9"
+scikit-image==0.17.2
 scipy==1.5.4
 SimpleITK==2.0.2rc2.dev785+g8ac4f
 six==1.16.0
 tifffile==2020.9.3
-traits==6.3.2
-traitsui==7.4.0
+traits==6.4.1
+traitsui==7.4.3
 treelib==1.6.1
 typing_extensions==4.1.1
-urllib3==1.26.11
-vtk==9.1.0
-wslink==1.6.6
-yarl==1.7.2
+urllib3==1.26.14
 zipp==3.6.0

envs/requirements_py37

@@ -1,69 +1,56 @@
 --extra-index-url https://pypi.fury.io/dd8/
-aiohttp==3.8.3
-aiosignal==1.2.0
 appdirs==1.4.4
-apptools==5.2.0
-async-timeout==4.0.2
-asynctest==0.13.0
-attrs==22.1.0
 bg-atlasapi @ https://github.com/brainglobe/bg-atlasapi/archive/dbecd16b2f63a8e167543f3358452a756bad0e64.tar.gz
 bg-space==0.6.0
-boto3==1.24.93
-botocore==1.27.93
-certifi==2022.9.24
-charset-normalizer==2.1.1
+boto3==1.26.83
+botocore==1.29.83
+certifi==2022.12.7
+charset-normalizer==3.0.1
 click==8.1.3
-commonmark==0.9.1
-configobj==5.0.6
 cycler==0.11.0
-envisage==6.1.0
-fonttools==4.37.4
-frozenlist==1.3.1
-future==0.18.2
+fonttools==4.38.0
+future==0.18.3
 idna==3.4
 imagecodecs==2021.11.20
-imageio==2.22.2
-importlib-metadata==5.0.0
-importlib-resources==5.10.0
+imageio==2.26.0
+importlib-metadata==6.0.0
+importlib-resources==5.12.0
 javabridge==1.0.19.post4+gbebed64
 jmespath==1.0.1
 kiwisolver==1.4.4
+markdown-it-py==2.2.0
 matplotlib==3.5.3
 matplotlib-scalebar==0.8.1
-mayavi==4.8.1
+mdurl==0.1.2
 meshio==5.3.4
-multidict==6.0.2
 networkx==2.6.3
 numpy==1.21.6
-packaging==21.3
+packaging==23.0
 pandas==1.3.5
-Pillow==9.2.0
+Pillow==9.4.0
 pyamg==4.2.3
-pyface==7.4.2
-Pygments==2.13.0
+pyface==7.4.4
+Pygments==2.14.0
 pyparsing==3.0.9
-PyQt5==5.15.7
+PyQt5==5.15.9
 PyQt5-Qt5==5.15.2
-PyQt5-sip==12.11.0
+PyQt5-sip==12.11.1
 python-bioformats==4.0.5.post2+g51eb88a
 python-dateutil==2.8.2
-pytz==2022.5
+pytz==2022.7.1
 PyWavelets==1.3.0
 PyYAML==6.0
-requests==2.28.1
-rich==12.6.0
+requests==2.28.2
+rich==13.3.1
 s3transfer==0.6.0
 scikit-image==0.19.3
 scipy==1.7.3
 SimpleITK==2.0.2rc2.dev785+g8ac4f
 six==1.16.0
 tifffile==2021.11.2
 traits==6.4.1
-traitsui==7.4.1
+traitsui==7.4.3
 treelib==1.6.1
-typing_extensions==4.4.0
-urllib3==1.26.12
-vtk==9.2.2
-wslink==1.8.4
-yarl==1.8.1
-zipp==3.9.0
+typing_extensions==4.5.0
+urllib3==1.26.14
+zipp==3.15.0