Skip to content

Releases: connectomicslab/connectomemapper3

2ce5619
Compare
Choose a tag to compare

Connectome Mapper 3 implements, in accordance to the BIDS-App standard, full anatomical, diffusion, and resting/state functional MRI processing pipelines, from raw T1 / DWI / BOLD data to multi-resolution brain parcellation with corresponding connection matrices, based on a new version of the Lausanne parcellation atlas (Cammoun et al, 2012), aka Lausanne2018.

This version mainly addresses all points raised by the JOSS review.

What's Changed

Updates

Bug fix

  • Add missing cmp.stages.eeg to setup_pypi.py. (PR #166)
  • Add missing package data for parcellation in setup_pypi.py. (PR #182)
  • Use HTTPS instead of SSH for datalad clone in notebooks . (PR #181)
  • Add missing condition to handle custom BIDS files with session. (PR #183)
  • Integrate fix from Napari project for issues with menubar on Mac. (PR #174)
  • Use the most recent PyQt5 instead of PySide2 (older) for graphical backend of cmpbidsappmanager, which provides a fix to run Qt-based GUI on MacOSX Big Sur. (PR #188)

Documentation

  • Correct conda env create instruction in the README. (PR #164)
  • Refer to contributing guidelines in the README. (PR #167)
  • Use sphinx-copybutton extension in the docs. (PR #168)
  • Add notes about docker image and conda environment size and time to download. (PR #169)

JOSS paper

  • Integrate minor wording tweaks by @jsheunis. (PR #162)
  • Add higher level summary and rename the old summary to "Overview of Functionalities". (PR #175)

License

  • The license has been updated to a pure 3-clause BSD license to comply with JOSS. (PR #163)

Software development life cycle

  • Migrate ubuntu 16.04 (now deprecated) to 20.04 on CircleCI. (PR #172)

Contributors

More...

Full Changelog: v3.0.3...v3.0.4

Compare
Choose a tag to compare

Connectome Mapper 3 implements, in accordance to the BIDS-App standard, full anatomical, diffusion, and resting/state functional MRI processing pipelines, from raw T1 / DWI / BOLD data to multi-resolution brain parcellation with corresponding connection matrices, based on a new version of the Lausanne parcellation atlas (Cammoun et al, 2012), aka Lausanne2018.

This version mostly introduces the new pipeline dedicated to EEG modality with a tutorial, updates Freesurfer to 7.1.1, and adds a new tutorial that shows how to analyze the CMP3 connectomes.

What's Changed

New features

  • CMP3 provides a new pipeline cmp.pipelines.functional.eeg.EEGPipeline dedicated to EEG modality with a collection of interfaces and methods implemented by the following modules: cmtklib.eeg, cmtklib.interfaces.eeg, cmtklib.interfaces.mne, and cmtklib.interfaces.pycartool.
    See PR #82 for more details.

Updates

  • Freesurfer has been updated from 6.1.0 to 7.1.1. See PR #147 for more details.

Bug fix

  • FIX: List of outputs are empty in inspector window of the parcellation and fmri_connectome stages.
    See PR #145 for more details.
  • Correct way GM mask is generated and clean code in cmtklib/parcellation.py.
  • Add interface to copy 001.mgz using hardlink.

Documentation

  • Add documentation of new classes and functions introduced by the EEG pipeline.
  • Add two ipython notebooks in docs/notebooks that are integrated directly in the docs with nbsphinx:
    • analysis_tutorial.ipynb: Show how to interact, analyze, and visualize CMP3 outputs.
    • EEG_pipeline_tutorial.ipynb: Show how to use the new API dedicated to the EEG pipeline.

Contributors

More...

Please check the main PR #146 page for more details.

Compare
Choose a tag to compare

Connectome Mapper 3 implements, in accordance to the BIDS-App standard, full anatomical, diffusion, and resting/state functional MRI processing pipelines, from raw T1 / DWI / BOLD data to multi-resolution brain parcellation with corresponding connection matrices, based on a new version of the Lausanne parcellation atlas (Cammoun et al, 2012), aka Lausanne2018.

This release introduces the capability to estimate carbon footprint of CMP3 execution and fix problems of conflicts during the creation of the conda environment.

What's changed

New features

  • Allow the estimation of the carbon footprint while using the BIDS App python wrappers and the GUI. Estimations are conducted using codecarbon. All functions supporting this features have been implemented in the new module cmtklib.carbonfootprint.

    See PR #136 for more details.

Code changes

  • Creation of init_subject_derivatives_dirs() for AnatomicalPipeline, DiffusionPipeline, and fMRIPipeline that return the paths to Nipype and CMP derivatives folders of a given subject / session for a given pipeline. This removed all the implicated code from the process() method and improve modularity and readability. In the future, the different functions could be merged as there is a lot of code duplication between them.
  • AnatomicalPipeline, DiffusionPipeline, and fMRIPipeline workflows are run with the MultiProc plugin.

Bug fix

  • Major update of the conda/environment.yml and conda/environment_macosx.yml to correct the problems of conflicts in the previous version, as reported in issue #137. This has resulted in the following package updates:

    • pip: 20.1.1 -> 21.3.1
    • numpy: 1.19.2 -> 1.21.5
    • matplotlib: 3.2.2 -> 3.5.1
    • traits: 6.2.0 -> 6.3.2
    • traitsui: 7.0.0 -> 7.2.0
    • graphviz: 2.40.1 -> 2.50.0
    • configparser: 5.0.0 -> 5.2.0
    • git-annex: 8.20210127 -> 8.20211123
    • pyside2: 5.9.0a1 -> 5.13.2
    • indexed_gzip: 1.2.0 -> 1.6.4
    • cvxpy: 1.1.7 -> 1.1.18
    • fsleyes: 0.33.0 -> 1.3.3
    • mrtrix3: 3.0.2 -> 3.0.3
    • duecredit: 0.8.0 -> 0.9.1
    • mne: 0.20.7 -> 0.24.1
    • datalad: 0.14.0 -> 0.15.4
    • datalad-container: 1.1.2 -> 1.1.5
    • statsmodels: 0.11.1 -> 0.13.1
    • networkx: 2.4 -> 2.6.3
    • pydicom: 2.0.0 -> 2.2.2

    See commit 483931f for more details.

Documentation

  • Add description of carbon footprint estimation feature.
  • Improve description on how to use already computed Freesurfer derivatives.

Misc

  • Add bootstrap CSS and jquery JS as resources to cmtklib/data/report/carbonfootprint. They are used to display the carbon footprint report in the GUI.
  • Clean the resources related to parcellation in cmtklib/data/parcellation and rename all files and mentions of lausanne2008 to lausanne2018.
  • Removed unused cmtklib.interfaces.camino, cmtklib.interfaces.camino2trackvis,
    and cmtklib.interfaces.diffusion modules
  • Create and use a .coveragerc file to set the run of Coverage.py with --concurrency=multiprocessing
    to be allow to track code inside Nipype interfaces, now managed by multiprocessing.
  • Specify to Coverage.py with # pragma: no cover part of the code we know it won’t be executed

Code style

  • Correct a number of code style issues with class names.

Contributors

More...

Please check the main PR #140 page for more details.

Full Changelog: v3.0.1...v3.0.2

Compare
Choose a tag to compare

Connectome Mapper 3 implements, in accordance to the BIDS-App standard, full anatomical, diffusion, and resting/state functional MRI processing pipelines, from raw T1 / DWI / BOLD data to multi-resolution brain parcellation with corresponding connection matrices, based on a new version of the Lausanne parcellation atlas (Cammoun et al, 2012), aka Lausanne2018.

This correspond to the second official version release, which is mostly a bug fix and code refactoring release that allows the python packages of Connectome Mapper 3 to be available on PyPI. It incorporates Pull Request #132 and includes the following changes.

What's changed

Bug fix (CI)

  • Rename the project name in setup.pyand setup_pypi.py from cmp to connectomemapper. The cmp project name was already existing on PyPI, that caused continuous integration on CircleCI to fail during the last v3.0.0 release, while uploading the python packages of CMP3 to PyPI.

Code refactoring

  • Make cmp.bidsappmanager.gui.py more lightweight by splitting the classes defined there in different files.
    (See Issue #129 for more discussion details)

  • Split the create_workflow() method of the RegistrationStage into the create_ants_workflow(), create_flirt_workflow(), and create_bbregister_workflow().
    (See Issue #95 for more discussion details)

Code style

  • Correct a number of code style issues with class names

Contributors

More...

Please check the main pull request 132 page for more details.

Best wishes for 2022!!! 🍾 🥳

Compare
Choose a tag to compare

Connectome Mapper 3 implements, in accordance to the BIDS-App standard, full anatomical, diffusion, and resting/state functional MRI processing pipelines, from raw T1 / DWI / BOLD data to multi-resolution brain parcellation with corresponding connection matrices, based on a new version of the Lausanne parcellation atlas (Cammoun et al, 2012), aka Lausanne2018.

This corresponds to the first offical release of Connectome Mapper 3 ! 🎄🎁

What's changed

New features

  • CMP3 can take custom segmentation (brain, white-matter, gray-matter and CSF masks, Freesurfer's aparcaseg - used for ACT for PFT) and parcellation files as long as they comply to BIDS Derivatives specifications, by providing the label value for the different entity in the filename. This has led to the creation of the new module cmtklib.bids.io, which provides different classes to represent the diversity of custom input BIDS-formatted files.
    (PR #88)

  • CMP3 generates generic label-index mapping .tsv files along with the parcellation files, in accordance to BIDS derivatives. This has led to the creation of the ~cmtklib.bids.utils.CreateBIDSStandardParcellationLabelIndexMappingFile and ~cmtklib.bids.utils.CreateCMPParcellationNodeDescriptionFilesFromBIDSFile interfaces, which allows us to create the BIDS label-index mapping file from the parcellation node description files employed by CMP3 (that includes _FreeSurferColorLUT.txt and _dseg.graphml), and vice versa.

  • CMP3 provide python wrappers to the Docker and Singularity container images connectomemapper3_docker and connectomemapper3_singularity that generate and execute the appropriate command to run the BIDS App.
    (PR #109, PR #115, PR #130)

Major changes

  • Lausanne2018 parcellation has completely replaced the old Lausanne2008 parcellation. In brief, the new parcellation was introduced to provide (1) symmetry of labels between hemispheres, and (2) a more optimal generation of the volumetric parcellation images, that now are generated at once from .annot files. This fixes the issue of overwritten labels encountered by in the process of creating the Lausanne2008 parcellation. Any code and data related to Lausanne2008 has been removed. If one still wish to use this old parcellation scheme, one should use CMP3 v3.0.0-RC4.

Pipeline Improvements

  • Better handle of existing Freesurfer outputs. In this case, CMP3 does not re-create the mri/orig/001.mgz and connect the reconall interface anymore.

  • Creation of 5TT, gray-matter / white-matter interface, and partial volume maps images are performed in the preprocessing stage of the diffusion pipeline only if necessary.

Output updates

  • Directories for the derivatives produced by cmp ([cmp]{.title-ref}, freesurfer, nipype were renamed to cmp-<cmp_version>, freesurfer-<freesurfer_version>, and nipype-<nipype_version> to comply with BIDS 1.4.0+. (PR #3 (fork))

Code refactoring

  • Creation in AnatomicalPipeline, DiffusionPipeline, fMRIPipeline of create_datagrabber_node()and create_datasinker_node() methods to reduce the code in create_workflow().

  • The run(command) function of cmp.bidsappmanager.core has been moved to cmtklib.process, which is used by the python wrappers in cmp.cli.

Code Style

  • Clean code and remove a number of commented lines that are now obsolete. Code related to the connection of nodes in the Nipype [Workflow]{.title-ref} adopts a specific format and are protected from being reformatted by BLACK with the # fmt: off and # fmt: on tags.

Documentation

  • Add instructions to use custom segmentation and parcellation files as inputs.

  • Add description in contributing page of format for code related to the connection of the nodes in a Nipype Workflow.

  • Add instructions to use the python wrappers for running the BIDS App.
    (PR #115)

  • Add notification about the removal of the old Lausanne2008 parcellation, and remove any other mentions in the documentation.

Software container

  • Define multiple build stages in Dockerfile, which can be run in parallel at build with BUILDKIT.
    (PR #88)

Software development life cycle

  • Update the list of outputs of circleci tests with the new names of directories produced by cmp in output_dir/.

  • Following major changes in the pricing plans of CircleCI but also to
    improve its readability, .circleci/config.yml has been
    dramatically refactored, including:

    • Use BUILDKIT in docker build to take advantage of the multi-stage build
    • Reordering and modularization of the tests:
      • tests 01-02 (Docker): anatomical pipeline for each parcellation scheme
      • tests 03-06 (Docker): diffusion pipeline for dipy/mrtrix deterministic/probabilistic tractography
      • tests 07-08 (Docker): fMRI pipeline for FLIRT and BBRegistration registrations
      • test 09 (Singularity): anatomical pipeline for Lausanne2018 scheme
    • Creation of commands for steps that are shared between jobs to reduce code duplication
      (PR #88)

Contributors

More

Please check the main pull request 88 page for more details.

Compare
Choose a tag to compare

This is the fourth release candidate of Connectome Mapper (v3.0.0-RC4) which merges PR #74.

Complete list of changes with respect to previous v3.0.0-RC3:

  • MAINT: Set debug=False in methods of cmtklib/config.py (9 hours ago) - commit 249e4e5
  • DOC: Update release date in changes.rst and copyright year in readme [skip ci] (9 hours ago) - commit de1da17
  • Merge pull request #74 from connectomicslab/release/v3.0.0-RC4 (9 hours ago) - commit 31f1576
  • CI: Remove {{ file }} in send_codecov_report (2 days ago) - commit 4a78d49
  • CI: Add missing docker spec in send_codecov_report (2 days ago) - commit 0bb0a26
  • CI: Fix indentation error in config.yml (2 days ago) - commit 755b2a3
  • CI: Send reports to Codecov (2 days ago) - commit 23b4e51
  • CI: Send coverage report to codecov (2 days ago) - commit 26eca00
  • REF: Review BIDS naming to differentiate parcellation from different atlas and scale (2 days ago) - commit d6a82d8
  • TEST: Remove duplicated lines in list of outputs of test-08 [skip ci] (2 days ago) - commit f74f721
  • TEST: Re-enable check of outputs for all tests (1-8) (2 days ago) - commit 339a23d
  • CI: Update lists of outputs for tests 07 and 08 (3 days ago) - commit 75456e8
  • CI: Remove test-09 that was exactly the same than test-01 (3 days ago) - commits d093794 9ee13a7
  • DOC: Review header level in outputs.rst [skip ci] (3 days ago) - commit 0f3b68e
  • DOC: Update index.rst [skip ci] (3 days ago) - commit 4ade5c2
  • DOC: Update changes.rst [skip ci] (3 days ago) - commits 3361395 cf522f2 adae02a 3fe0d4a a842f90 cd42a09
  • UPD: Update dataset_description.json of derivatives to conform to BIDS 1.4.0 (3 days ago) - commit 449d9f6
  • DOC: Review layout in outputs.rst [skip ci] (3 days ago) - commit eff219d
  • DOC: Update outputs.rst with new BIDS naming convention [skip ci] (3 days ago) - commit 02b093e
  • DOC: Review docstrings in files for pipelines (3 days ago) - commit 466fdcd
  • FIX: Remove debug option from check_input of fmri pipeline (3 days ago) - commit 1111ac9
  • DEL: Remove obsolete Check_Input_Notifications classes (3 days ago) - commit 0fa37bb
  • CI: Updated the list of outputs for all tests except for fmri (tests 7 and 8) (3 days ago) - commit 9204cb3
  • FIX: Correct typos (4 days ago) - commit bb72833
  • TEST: Commented all test for output differences in circleci config (4 days ago) - commit 740ed90
  • REF: Review BIDS naming using atlas as keyword type and use res-scale to differentiate scales (4 days ago) - commit 5ab54f0
  • FIX: Correct typos in substitution in the datasinker of fmri pipeline (4 days ago) - commit 6e8c3ab
  • DEL: Remove old commented code in fMRI.py (4 days ago) - commit c903395
  • MAINT: Review code to use pyside2 (GUI) (4 days ago) - commit 62f3ef3
  • DOCKER: Update to ubuntu:xenial-20210114 for FSL5.0 (5 days ago) - commits 19b7c86 3037a8e
  • DOCKER: Move installation of perl in first run (5 days ago) - commit 4e9e6b6
  • DOCKER: Update to ubuntu 18.04 (5 days ago) - commit cfc032d
  • DOCKER: Install perl to make freesurfer hippo and subfields happy (5 days ago) - commit 56c9a1e
  • UPD: Update to use pyside2 (qt) (5 days ago) - commit cbc9b60
  • DOC: Update installation.rst with a note on how to update CMP3 (5 days ago) - commit 5d29b70
  • DOC: Update changes.rst (5 days ago) - commit 866fbc3
  • STY: Correct remaining code style issues (5 days ago) - commit 22bd03e
  • FIX: Better handle float as string for ants_precision_type (6 days ago) - commit fc65400
  • FIX: Better handle float as string for ants_precision_type (6 days ago) - commit 7ceb98e
  • DEBUG: Set debug=True in set_pipeline_attributes_from_config() (6 days ago) - commit 58f11b9
  • FIX: Better handle float as string for ants_precision_type (6 days ago) - commit 5d91110
  • DEBUG: Set debug=True in save_configparser_as_json() (6 days ago) - commit 9c3046f
  • MAINT: Clean code and prints in connectomemapper3 script (6 days ago) - commit 380fedc
  • MAINT: Clean print in define_inspect_outputs() of fmriconnectome stage (6 days ago) - commit 3933c9b
  • MAINT: Clean code and prints in define_inspect_outputs() for all stages (6 days ago) - commit b9644ea
  • MAINT: Remove old commented code and review code layout in run.py (6 days ago) - commit f9fe9f5
  • REF: Creation of sub-methods to modularize clean_cache and reduce duplication (6 days ago) - commit b4ad67d
  • CI: Show python version in the docker image used in build-docker on circleci (6 days ago) - commit 9b3d5cc
  • FIX: Remove fstring for copyright to make python on circleci happy (6 days ago) - commit c30d8f7
  • MAINT: Review output generated by BIDS App in run.py (9 days ago) - commit 941a981
  • MAINT: Clean output print at loading of the GUI (9 days ago) - commit c9e6950
  • MAINT: Clean output print for copyright and config save/load methods (9 days ago) - commit a3e8190
  • MAINT: Clean output print and disable debug mode for config save/load methods (9 days ago) - commit e26627a
  • ENH: Remove log_visualization and circular_layout from configuration file (9 days ago) - commit c1d8b35
  • MAINT: Clean output print (9 days ago) - commit be0f0c9
  • MAINT: Review prints in config load/save (9 days ago) - commit 8ef9c2e
  • FIX: Review loading of dict from json (9 days ago) - commit 93e9713
  • FIX: Review conversion from init to json (9 days ago) - commit 8037195
  • FIX: Handle the loading of config parameters (9 days ago) - commit 33890ee
  • FIX: Handle differently tuple in the loading of config parameters (9 days ago) - commit a17b080
  • FIX: Save differently dict type of config parameters (9 days ago) - commit 8702682
  • FIX: Handle differently tuple in the loading of config parameters (9 days ago) - commit dafda7d
  • FIX: Handle differently list in the loading of config parameters (9 days ago) - commit 9db2c0b
  • FIX: Remove list to be handled in the loading of configuration parameter types (9 days ago) - commit 2075e61
  • MAINT: Review info message printed at launch of cmpbidsappmanager (9 days ago) - commit 00a32b5
  • MAINT: Review info message printed at launch of cmpbidsappmanager (9 days ago) - commit abe74b9
  • MAINT: Update main copyright line layout (9 days ago) - commit 0e62eff
  • MAINT: Review cmpbidsappmanager and try to use qt (pyside2) (9 days ago) - commit 8c1f4c2
  • MAINT: Review all print output generated by the GUI (9 days ago) - commit 3a34b82
  • MAINT: Remove obsolete methods and add debug mode for extra prints in cmtklib.util.py (9 days ago) - commit 7855b81
  • WIP: Better handle loading of configuration parameter types (9 days ago) - commits 10d8b7c d8f0b38 f5b394e 9bd70a5 26dbd5b fb9b722 fc6f6e7 36976ec 8f2e679 cf2fb4f 4b3ef59 18c0a05 da78108
  • FIX: Error in creating docker image caused by dbus with python2.7 (10 days ago) - commit 259f1cf
  • DEL: Remove a number of files now obsolete (10 days ago) - commit 97beaba
  • DOC: Update copyright (10 days ago) - commit 407d5d1
  • DOC: Update footer with special authors/version/copyright section (10 days ago) - commit 84e0a42
  • FIX: Remove cmp/bidsappmanager from .dockerignore (10 days ago) - commit 02721d2
  • FIX: Set cache for eggs before pip install (10 days ago) - commit 69ce438
  • DOC: Improve runonhpc.rst (10 days ago) - commit fab2bf6
  • DOC: Double the \ in commands of runonhpc.rst (10 days ago) - commit 2ee17cb
  • DOC: Improve command rendering in runonhpc.rst (10 days ago) - commit 7ab385c
  • DOC: Improve installation.rst (10 days ago) - commit b23cd15
  • DOC: Edit installation.rst (10 days ago) - commit 94c8237
  • DOC: Edits in tutorials (10 days ago) - commit bc84b13
  • DOC: Add prerequisites section to tutorials (10 days ago) - commit 90e7ec3
  • REF: Rename ubuntu16.04 to docker and related changes in Dockerfile (10 days ago) - commit 6ab48e5
  • DEL: Remove files related to obsolete main docker image (10 days ago) - commit 531ddf5
  • CI: Deleted run task related to removed setup_cmp.py (10 days ago) - commit ac57b6b
  • ENH: Merge the two setup files into one to make pip happy (10 days ago) - commit c0d76e5
  • WIP: Review how to retrieve parameters of anatomical pipeline (11 days ago) - commit d8d49a8
  • FIX: Review how to retrieve parameters of anatomical pipeline (11 days ago) - commit 88cb5e5
  • FIX: Create folder with right permissions and set PYTHON_EGG_CACHE in Dockerfile (11 days ago) - commit 2aeb6ca
  • ENH: Convert auto config files (INI) to JSON with cmpbidsappmanager (11 days ago) - commit eb30d03
  • MAINT: Set debug to False in cmtklib.config methods (11 days ago) - commit 3d20fc0
  • MAINT: Add extra blank line at the file end (11 days ago) - commit 8a95c43
  • MAINT: Edit a number of print outputs of cmpbidsappmanager and config (11 days ago) - commit 3b47bdb
  • WIP: Review how existing JSON file are loaded and saved (11 days ago) - commits 283e844 7045924
  • FIX: Add "none" to Enum for slice_timing in fmri_preprocessing stage (11 days ago) - commit b0ac394
  • FIX: Review how existing JSON file are loaded and saved (11 days ago) - commit a58aa10 d19004a 16e8875 f1e4295 9d544f3 a4125c3 6ad9e4b d531b68 3b661b4 f116a7e
  • ENH: Skip "_editor" attributes of stages in saved config (11 days ago) - commit 59d1afe
  • MAINT: Remove comments for freesurfer reconall node and set freesurfer_args to "" (11 days ago) - commit 51c929f
  • MAINT: Remove option to specify custom segmentations (11 days ago) - commit f927b90
  • DEBUG: Add additional debug prints in cmtklib/config.py (11 days ago) - commit 294fe0f
  • MAINT: Clean more prints generated by the config functions and the GUI (11 days ago) - commit 0ade58d
  • ENH: Use the new color print methods (11 days ago) - commit 8e0be3d
  • MAINT: Clean code and improve code style (11 days ago) - commit ef5582e
  • MAINT: Set debug argument to False when starting cmpbidsappmanager (11 days ago) - commit 6d649aa
  • MAINT: Rename package names in imports for pipelines in bidsappmanager/project.py (11 days ago) - commit 6d66da6
  • MAINT: Remove remaining comments referring to fix_dataset_directory_in_pickles (11 days ago) - commit 67e9556
  • ENH: Add debug boolean argument to save_configparser_as_json (11 days ago) - commit 9437cd6
  • ENH: Add utility method to print in color in cmtklib/util.py (11 days ago) - commit 1aba8fc
  • MAINT: Remove all comments referring to fix_dataset_directory_in_pickles (11 days ago) - commit c7b05c8
  • DOC: Updates changes.rst (12 days ago) - commit a408416
  • DOC: Improve datalad tutorial (12 days ago) - commit eebdce5
  • DOC: Few fixes in datalad tutorial (12 days ago) - commit 1404f24
  • DOC: Updates changes.rst (12 days ago) - commit bdd7b9e
  • Merge pull request #78 from sebastientourbier/release/v3.0.0-RC4/enh/pypi_setup (12 days ago) - commit 886c1c6
  • STY: Fix code style issues in refactored scripts (13 days ago) - commits f0e8c80 433b8f2
  • MAINT: Remove try/except for imports of matplotlib and mne in showmatrix_gpickle [skip ci] (13 days ago) - commit 6fd0f8b
  • DOC: Update changes.rst [skip ci] (13 days ago) - commit 4bd84c0
  • CI: Update to use sudo for "pip3 uninstall -y cmp" (13 days ago) - commit bd78d6d
  • CI: Remove installation of pybids in test-python-install job (13 days ago) - commit 4f42800
  • DOC: Update installation.rst with "pip install ." command (13 days ago) - commit 6ce9cb0
  • CI: Remove "Smoke Test Install connectomemapper3" from test-python-install (13 days ago) - commit 388ec27
  • CI: Install missing pybids for smoke test of connectomemapper3 (13 days ago) - commit 472ef21
  • CI: add sudo to "python3 setup_cmp.py develop" (13 days ago) - commit da2ed79
  • MAINT: Remove shebang in cmp/cli scripts (13 days ago) - commit 5aa7489
  • DOC: Add docstring in cmp/cli init module (13 days ago) - commit 437f272
  • CI: Review test-python-install job in config.yml (13 days ago) - commit ef024cb
  • CHG: Rename setup files (13 days ago) - commit f017f8e
  • FIX: Add "cmp.cli" to list of packages in setup files (13 days ago) - commit 34deb93
  • CI: Update package name from cmp3 to cmp in pip3 un-/install (13 days ago) - commit 890c54b
  • MAINT: Update package name from cmp3 to cmp and review description in setup.py (13 days ago) - commit 40fab57
  • CI: Add smoke test for installation of connectomemapper3 script (13 days ago) - commit a3d705a
  • CI: Fix to "pip3 uninstall -y cmp3" (13 days ago) - commit e7287ef
  • CI: Remove deploy-pypi-release (13 days ago) - commit 18f29a8
  • DOC: Update changes.rst (13 days ago) - commit ab97e08
  • CI: Add job to test the PyPI distribution (13 days ago) - commit 217ef7f
  • MAINT: Add init to to new "cmp.cli" package/module (13 days ago) - commit 2e788a1
  • REF: Update paths to scripts to be installed by PypI for GUI (13 days ago) - commit ab6842f
  • MAINT: Add copyright in cmp/info.py (13 days ago) - commit 9696efd
  • REF: Move and refactor scripts to be installed by PyPI (13 days ago) - commit 6b3cf57
  • FIX: Remove "v" in VerifyVersionCommand of setup.py (13 days ago) - commit afc251f
  • REF: Review main setup_gui.py for installation with PIP (13 days ago) - commits 57b8936 18c8215
  • DOC: Updates changes.rst (2 weeks ago) - commits a891c4f 2daa3d5
  • ENH: Update data provenance tracking functionality with Datalad (2 weeks ago) - commit f2e4fda
  • DOC: Update tutorials [skip ci] (2 weeks ago) - commits 6f0a70b 3623c9d
  • DOC: Correct typo in tutorial on datalad [skip ci] (2 weeks ago) - commits 1017583 db9cd5d 28d14bb
  • DOC: Update tutorials [skip ci] (2 weeks ago) - commit d456d92
  • DOC: Correct typo in tutorial on datalad [skip ci] (2 weeks ago) - commit b00fcc2
  • VERSION: Revert back to v3.0.0-RC4 [skip ci] (2 weeks ago) - commit 55df9cc
  • DOC: Delete typo [skip ci] (2 weeks ago) - commit 49708aa
  • DOC: Adopt YODA in tutorial on Datalad [skip ci] (2 weeks ago) - commit 95968a6
  • DOC: Edit docs/datalad.rst [skip ci] (2 weeks ago) - commit 7f732d3
  • DOC: Edit style of files listed in tutorial on datalad [skip ci] (2 weeks ago) - commit 535ff7c
  • DOC: Improve tutorial on Datalad [skip ci] (2 weeks ago) - commits 4c6a72f 07d1219 10e92c3
  • DOC: Review description of --call-fmt in tutorial on Datalad [skip ci] (2 weeks ago) - commit cbcf1bd
  • DOC: Improve installation part in tutorial on Datalad [skip ci] (2 weeks ago) - commit 8c12038
  • DOC: Improve tutorial on Datalad [skip ci] (2 weeks ago) - commit 7f0afba
  • DOC: Improve docs of new JSON format for configuration files [skip ci] (2 weeks ago) - commit 1fe11fe
  • FIX: FileDialog are in 'open' mode for files in the BIDS App GUI (2 weeks ago) - commit 92d2f87
  • DEL: Remove freesurfer_subject_id_trait (2 weeks ago) - commit 02ac51c
  • MAINT: comment call to project.clean_cache() method after datalad run-containers (2 weeks ago) - commit cd4b7a6
  • DOC: Add comment (2 weeks ago) - commit c0c2aa8
  • ENH: Review docker run command to use current directory as bids root for datalad (2 weeks ago) - commit e8c2191
  • UPD: Update all configuration files to JSON in GUI (#76) [skip ci] (2 weeks ago) - commit c79353f
  • Merge branch 'release/v3.0.0-RC4' into enh/datalad (2 weeks ago) - commit dab82bf
  • DOC: Update changes.rst [skip ci] (2 weeks ago) - commit 130f217
  • DOC: Update --call-fmt in datalad.rst (2 weeks ago) - commit 01e4fc5
  • DOC: First draft of new datalad.rst (2 weeks ago) - commit b95416a
  • DOC: Edit datalad.rst (2 weeks ago) - commit 43dd101
  • Merge pull request #76 from connectomicslab/enh/json_configuration_files (2 weeks ago) - commit e063528
  • TEST: Update list of outputs for test 9 with .graphml connectome files (2 weeks ago) - commit 3c03615
  • MAINT: Add -t to docker run command for datalad add-containers (2 weeks ago) - commit bbcbfdb
  • MAINT: Modify datalad save messages (2 weeks ago) - commit fb480be
  • ENH: Add colors to datalad command and error prints (2 weeks ago) - commit d068ead
  • ENH: Use the option --update of datalad add-container (3 weeks ago) - commit d98c4e4
  • FIX: Add "mrtrix_tracking_config.sift = True" to ref_diffusion_config_2.ini (3 weeks ago) - commit 4241648
  • FIX: Add "mrtrix_tracking_config.sift = True" to ref_diffusion_config_1.ini (3 weeks ago) - commit 9893bad
  • TEST: Update list of outputs for test 2 with .mat and .graphml connectome files (3 weeks ago) - commit 44d2099
  • TEST: Update list of outputs for test 8 with .graphml connectome files (3 weeks ago) - commit f6cb731
  • DOC: Start updating Datalad documentation (3 weeks ago) - commit 3cd36dc
  • FIX: Substitute sebastientourbier/connectomemapper-bidsapp to {img} in --call-fmt of container with Datalad (3 weeks ago) - commit 4300583
  • FIX: Review code related to config files when calling datalad add/run-containers (3 weeks ago) - commit a015b67
  • FIX: Parsing std output of datalad command with run() (3 weeks ago) - commit ef02189
  • FIX: Add missing "" in datalad dataset description at creation (3 weeks ago) - commit 2c05aad
  • ENH: specify explicitly the directory for datalad dataset creation (3 weeks ago) - commit cb8bd65
  • MAINT: Correct typo in datalad save message (3 weeks ago) - commit 5538e0b
  • FIX: Add missing - to --call-fmt in datalad run-containers command (3 weeks ago) - commit 3e3efc4
  • DEL: Remove datalad-revolution [skip ci] (3 weeks ago) - commit 5819d02
  • UPD: Update version datalad and extension packages in environment_macosx.yml of the GUI [skip ci] (3 weeks ago) - commit aca4732
  • UPD: Update to latest version of git-annex in environment.yml of the GUI [skip ci] (3 weeks ago) - commit d73694a
  • UPD: Update version datalad and extension packages in environment.yml of the GUI (3 weeks ago) - commit 27fb813
  • ENH: Prevent settings the output_dir when data provenance tracking with datalad is enabled (3 weeks ago) - commit 7822ee2
  • VERSION: Change back to version RC3 for testing (3 weeks ago) - commit 38af423
  • UPD: Update all datalad commands in cmp/bidsappmanager/gui.py (3 weeks ago) - commit 530fc95
  • FIX: Review code to create graph edges to save fMRI connectome in graphml (3 weeks ago) - commit d8020c1
  • DEL: Remove code in comments that save the old INI configuration files (3 weeks ago) - commit a7fd118
  • DOC: Review docstrings in cmtklib/config.py (3 weeks ago) - commit f69e517
  • FIX: add missing argument to set_pipeline_attributes_from_config() in cmtklib/config.py (3 weeks ago) - commit 09446b8
  • FIX: review code of save_configparser_as_json() (3 weeks ago) - commit a87e50d
  • TEST: update list of outputs for test-07 with .graphml connectome files (3 weeks ago) - commit 0f403ee
  • CI: Improve code coverage by saving functional connectomes as graphml files in test-07 (3 weeks ago) - commit 6c572fe
  • TEST: update list of outputs for test-01 with .mat and .graphml connectome files and curvature (3 weeks ago) - commit fe02897
  • REF: Refactor code in cmtklib/config.py to reduce code-block duplication (3 weeks ago) - commit 7167484
  • CI: Remove modalities from configuration files of tests (3 weeks ago) - commit 8142e6e
  • STY: Review line splits (3 weeks ago) - commit d768cba
  • ENH: Write version that generated the json configuration file (3 weeks ago) - commit 6c7e0e4
  • STY: clean code in cmtklib/connectome.py (3 weeks ago) - commit 5dd018d
  • CI: Remove probtrackx from diffusion configuration files of tests (3 weeks ago) - commit 92bf8a8
  • MAINT: Delete all remaining code related to probtrackx (3 weeks ago) - commit 7f2ef15
  • FIX: Review code to save functional connectome as graphml files (3 weeks ago) - commit 3ee6081
  • MAINT: Remove cff format (python2 only) as possible connectome output format (3 weeks ago) - commit 1471875
  • CI: improve coverage of connectome.py by testing to save connectomes as mat and graphml files (3 weeks ago) - commit edebdd7
  • CI: improve coverage of connectome.py by testing to compute fiber curvature (3 weeks ago) - commit 11903df
  • MAINT: update shebang of run.py to #!/usr/bin/env python [skip ci] (3 weeks ago) - commit 47ad0e4
  • MAINT: update copyright year in run.py [skip ci] (3 weeks ago) - commit 6d55fc6
  • DOC: Add copyrights, usage and comments in script to build the doc [skip ci] (3 weeks ago) - commit f8e2e5f
  • DOC: Add copyrights, usage and comments in script to build the BIDS App [skip ci] (3 weeks ago) - commit 1b074d8
  • DOC: review docstrings of setup.py and setup_gui.py files [skip ci] (3 weeks ago) - commit fa91c37
  • WIP: comment modalities attributes in diffusion pipeline (3 weeks ago) - commit 7b78180
  • WIP: revert back unset attributes in json config (3 weeks ago) - commit 457eb1a
  • FIX: review unset attributes in json config (3 weeks ago) - commit ac11933
  • DOC: updated list of changes [skip ci] (3 weeks ago) - commit 7737fdc
  • DOC: started editing changes.rst for v3.0.0-RC4 release [skip] (3 weeks ago) - commit 68153e2
  • DOC: update usage and add note of adoption of json for config files (3 weeks ago) - commit 7e83f10
  • TST: update list of output with .json extension for config files (3 weeks ago) - commit 927c88e
  • MAINT: clean debug print (3 weeks ago) - commit 8374c7c
  • Merge pull request #75 from connectomicslab/enh/73_coverage (3 weeks ago) - commit 1395849
  • ENH: check configuration file format and convert old INI to new JSON format (3 weeks ago) - commit 5234587
  • MAINT: remove all code related to INI configuration files (3 weeks ago) - commit 256492f
  • ENH: Use JSON instead of INI configuration files (3 weeks ago) - commit ba2aefd
  • FIX: write correctly boolean in json config files [skip ci] (3 weeks ago) - commit af8881f
  • ENH: call check_stages_execution() and fill_stages_outputs() for all pipelines (3 weeks ago) - commit 74de627
  • ENH: created method check_stages_execution() to test has_run() and is_running of each stage (3 weeks ago) - commit 12101ec
  • FIX: add 'multishell' to list of diffusion_imaging_model (3 weeks ago) - commit 67f873b
  • STY: review code layout (3 weeks ago) - commit 299413a
  • STY: review code layout (3 weeks ago) - commit 9ce927f
  • MAINT: fix typo in code (3 weeks ago) - commit 11ea7c2
  • STY: review code layout (3 weeks ago) - commit 3b3909f
  • VERSION: update version in cmp/info.py (3 weeks ago) - commit 9468985

Auto-generated with

git log v3.0.0-RC3..HEAD --pretty=format:' * %s %Cgreen(%cr) - commit %Cred%h%Creset' --abbrev-commit
34ae80f
Compare
Choose a tag to compare

This is the third release candidate of Connectome Mapper (v3.0.0-RC3) which merges PR #62.

Complete list of changes with respect to previous v3.0.0-RC2-patch1:

  • Merge pull request #62 from connectomicslab/v3.0.0-RC3 (4 minutes ago) - commit 34ae80f

  • DOC: update release date in changes.rst [skip ci] (7 minutes ago) - commit 07baaf8

  • DOC: Update usage and version in README [skip ci] (8 minutes ago) - commit 2a07d54

  • DOC: update copyright [skip ci] (8 minutes ago) - commit 1e1916b

  • CI: push singularity image of release as latest TAG [skip ci] (3 hours ago) - commit d3f1062

  • DOC: corrected link to section Nipype outputs [skip ci] (3 hours ago) - commit 4f5ae91

  • DOC: add description of BIDS entities employed in CMP outputs [skip ci] (3 hours ago) - commit 6366cae

  • DOC: review Nipype section in bidsappmanager and add link to outputs for more details [skip ci] (4 hours ago) - commit 41415a1

  • DOC: correct code style issues with lists not properly rendered [skip ci] (4 hours ago) - commit 35aa6ca

  • DOC: update description of --number_of_threads parser argument [skip ci] (4 hours ago) - commit 9ba43cd

  • DOC: correct style issue [skip ci] (4 hours ago) - commit 2fd5b23

  • MAINT: clean Dockerfile (25 hours ago) - commit 58517aa

  • CI: add expected output list for tests 7, 8 and 9 and enable difference check (27 hours ago) - commit 43d0e92

  • DOC: update changes.rst (27 hours ago) - commit 6556007

  • Merge branch 'master' (v3.0.0-RC2-patch1) into v3.0.0-RC3 (28 hours ago) - commit 4eb3e6f

  • MAINT: removed commented lines (coverage-reporter) in .circleci/config.yml (2 days ago) - commit 0e4ae16

  • CI: Use manually Codacy Coverage Reporter (2 days ago) - commit c75d899

  • CI: remove deployment of latest tag image on singularity for space (3 days ago) - commit 08c4eb9

  • CI: clean codacy_coverage_report job (7 days ago) - commit a9aa57c

  • MAINT: update codacy-reporter circleci orb (7 days ago) - commit c5c4c03

  • FIX: try to set MKL_NUM_THREADS=1 and OMP_NUM_THREADS=1 in Dockerfile (8 days ago) - commit 3e76e5c

  • MAINT: revert to use dipy.tracking.utils.seeds_from_mask() (8 days ago) - commit 3b1804c

  • FIX: reviewed multithreading management to set only number of threads for Freesurfer and ANTs (8 days ago) - commit 80563b2

  • MAINT: reviewed print with fstring and correct comment style issues (8 days ago) - commit 256913a

  • FIX: typo in run.py (8 days ago) - commit 6a5166a

  • FIX: install and use threadpoolctl to limit the number of OpenMP threads used by Numpy (8 days ago) - commit 8848498

  • DEL: remove installation of threadpoolctl (8 days ago) - commit bb6437d

  • FIX: try to use dipy to set omp num threads (8 days ago) - commit d01a43b

  • FIX: install and use threadpoolctl to limit the number of OpenMP threads used by Numpy (8 days ago) - commit bd7730d

  • MAINT: remove os.environ.update(MKL_NUM_THREADS='1') in run.py (8 days ago) - commit d5162ec

  • FIX: set OMP_NUM_THREADS to 1 prior to dipy.utils.seeds_from_mask (8 days ago) - commit 72fa6b3

  • FIX: set MK_NUM_THREADS to 1 to make numpy.dot working ? (9 days ago) - commit 24844d2

  • FIX: review how to set OMP_NUM_THREADS (9 days ago) - commit da07fa1

  • DOC: correct description of number_of_threads in docstring (9 days ago) - commit b994d7d

  • MAINT: remove old implementation commented (9 days ago) - commit 267958d

  • FIX: move first "import numpy" after setting the multi-threading variables (9 days ago) - commit a14df63

  • DEBUG: changed print() to IFLOGGER.info() (9 days ago) - commit 1396c0f

  • FIX: make sure seeds array is int (in interfaces/dipy.py / seeds_from_mask()) (11 days ago) - commit aa14b2c

  • FIX: update numpy (11 days ago) - commit 5e10bee

  • DEBUG: add prints in seeds_from_mask() (11 days ago) - commit 2771c1d

  • FIX: PeaksAndMetrics.shm_coeff w.r.t Dipy 1.3.0 (2 weeks ago) - commit 8af0a50

  • MAINT: use internal seeds_from_mask() in DirectionGetterTractography (2 weeks ago) - commit 27adab3

  • FIX: update estimation of response for CSD following major changes in Dipy 1.X (2 weeks ago) - commit 7f78dc7

  • DEBUG: insert dipy code for seeds_from_mask (2 weeks ago) - commit f597807

  • FIX: give vector of seed densities to dipy seeds_from_mask() (2 weeks ago) - commit 7804d67

  • FIX: test to remove clipMask as dipy seeds_from_mask() is triggering Segmentation Fault (l. 438) (2 weeks ago) - commit 15c486c

  • CI: add tests using the new config files in config.yml (2 weeks ago) - commit 2580992

  • CI: add fMRI config for testing FSL FLIRT, global nuisance regression, linear detrending and scrubbing (2 weeks ago) - commit f5a5b19

  • CI: add diffusion config for testing FLIRT co-registration and tractogram filtering with MRtrix3 SIFT (2 weeks ago) - commit 52a53ad

  • MAINT: reviewed code layout and prints with f-string in dipy.py (2 weeks ago) - commit fb04560

  • UPD: reverted back to ANTs 2.2.0 and reviewed comment style (2 weeks ago) - commit 9567877

  • MAINT: code style (2 weeks ago) - commit be114f3

  • UPD: update interface in dipy.py for EudXTracking with Tensor model w.r.t major Dipy 1.X changes (2 weeks ago) - commit 7b5bede

  • FIX: uncommented debug option and set debug to False for dwibiascorrect (2 weeks ago) - commit 3b79536

  • FIX: comment debug option in mrtrix dwibiascorrect that was raising errors after update to mrtrix 3.0.2 (2 weeks ago) - commit a156bd9

  • DOC: correct typo in docstring (2 weeks ago) - commit 48196a3

  • MAINT: add {} in environment variables with underscores (2 weeks ago) - commit b1b5f3c

  • Merge remote-tracking branch 'origin/v3.0.0-RC3' into v3.0.0-RC3 (2 weeks ago) - commit 9136f16

  • DOC: corrected typos and image in the BIDS App execution window (2 weeks ago) - commit fe6cf8f

  • FIX: review denoising/biasfieldcorrection node connection in preprocessing.py (2 weeks ago) - commit 0b3e3e8

  • FIX: update ANTs to 2.3.1 (2 weeks ago) - commit ad5f054

  • DOC: add the new images used in bidsappmanager.rst [skip ci] (3 weeks ago) - commit fa79ec0

  • DOC: updated images in bidsappmanager.rst [skip ci] (3 weeks ago) - commit 945dbfc

  • UPD: update dwibiascorrect command following change in mrtrix 3.0.2 (3 weeks ago) - commit e0b6569

  • DOC: updated instructions in bidsappmanager.rst [skip ci] (3 weeks ago) - commit 224ae31

  • DOC: correct conda activate command in bidsappmanager.rst [skip ci] (3 weeks ago) - commit 3739d82

  • FIX: unterminated quoted string error raised by CI (3 weeks ago) - commit f04b9d1

  • MAINT: reviewed installation of networkx (3 weeks ago) - commit 6072e30

  • REFACT: install mrtrix3 using conda (3 weeks ago) - commit 669c45e

  • UPD: update mrtrix to 3.0.2 in dockerfile (3 weeks ago) - commit 22d1d7e

  • UPD: update conda env with Nipype 1.5.1 (3 weeks ago) - commit c36d3d8

  • UPD: update conda env with dipy 1.3.0 and cvxpy 1.1.7 (3 weeks ago) - commit be9da76

  • MAINT: clean BIDSApp entrypoint script run_cmp3.sh [skip ci] (3 weeks ago) - commit 7d0ed0b

  • VERSION: update to v3.0.0-RC3 (3 weeks ago) - commit e66cc4d

  • STYLE: improved code style for connectomemapper3 cmd generation (3 weeks ago) - commit 562afbd

  • ENH: add color for warning and error prints during BIDS App settings check [skip ci] (3 weeks ago) - commit 9962617

  • FIX: print new attributes relative to RNG and ITK threads during BIDS App setting check [skip ci] (3 weeks ago) - commit 16bfa58

  • MAINT: use fstring to print summary of BIDS App settings check [skip ci] (3 weeks ago) - commit 0b7d42f

  • MAINT: correct code style [skip ci] (3 weeks ago) - commit 6edcf5c

  • DOC: add link to git-annex install page [skip ci] (3 weeks ago) - commit 20aab0d

  • DOC: add note to checkout the master branch if bugs in the GUI were fixed after version release [skip ci] (3 weeks ago) - commit 9119b84

  • DOC: updated installation instructions of conda environment on Mac [skip ci] (3 weeks ago) - commit 3fb0d50

  • ENH: add conda environment for macosx where git-annex has been removed (3 weeks ago) - commit 3cdee53

    Auto-generated with

    git log v3.0.0-RC2-patch1..HEAD --pretty=format:' * %s %Cgreen(%cr) - commit %Cred%h%Creset' --abbrev-commit
    

Summary of changes is available at the documentation.

This version fixes bugs in the second release candidate of Connectome Mapper 3 (v3.0.0-RC2).
In particular, it includes:

Bug fixes

  • Fix the error to save connectome in GraphML format reported in #65 (PR #66).

Software development life cycle

  • Remove publication of the Singularity image to sylabs.io when the master branch is updated for the sake of space (11GB limit)

Commits

  • CI: remove publication of latest tag image on sylabs.io for space (2 days ago) - commit c765f79
  • Merge pull request #66 from connectomicslab/v3.0.0-RC2-hotfix1 (3 days ago) - commit 0a2603e
  • FIX: update g2.node to g2.nodes when saving connectomes as graphml (fix #65) (6 days ago) - commit d629eef
  • FIX: enabled/disabled gray-out button "Run BIDS App" with Qt Style sheet [skip ci] (3 weeks ago) - commit 10e78d9
  • MAINT: removed commented lines in cmpbidsappmanager/gui.py [skip ci] (3 weeks ago) - commit 4cc11e7
  • FIX: check availability of modalities in the BIDS App manager window [skip ci] (3 weeks ago) - commit 80fbee2
  • MAINT: update copyright year [skip ci] (3 weeks ago) - commit f7d0ffb
  • CI: delete previous container with latest TAG on sylabs.io [skip ci] (4 weeks ago) - commit 15c9b18
  • DOC: update tag to latest in runonhpc.rst [skip ci] (4 weeks ago) - commit 3165bcc
  • CI: comment lines related to version for singularity push (4 weeks ago) - commit 3952d46
Compare
Choose a tag to compare

This is the second release candidate v3.0.0-RC2 of Connectome Mapper which merges PR #45.

Summary of changes is available at the documentation.

Complete list of changes with respect to previous 3.0.0-RC1:

  • CI: fix double to single quotes in deploy_singularity_release [skip ci] (2 minutes ago) - commit 7bbac75
  • Merge remote-tracking branch 'origin/master' [skip ci] (3 hours ago) - commit 237596b
  • VERSION: update release date in cmp/info.py [skip ci] (3 hours ago) - commit 5c0069c
  • DOC: update docker command in README [skip ci] (3 hours ago) - commit d262303
  • CI: update creation of singularity token for deploy_singularity (5 hours ago) - commit 818f3f5
  • Merge pull request #45 from connectomicslab/v3.0.0-RC2-dev (5 hours ago) - commit d9135ac
  • Merge pull request #58 from connectomicslab/57_documentation_v3.0.0-RC2-dev [skip ci] (5 hours ago) - commit cc47e0e
  • DOC: update description of new options in changes.rst [skip ci] (5 hours ago) - commit d1a3799
  • DOC: update release date in changes.rst [skip ci] (5 hours ago) - commit 8ff2b3a
  • DOC: fix sphinx version that might fix correct rendering of figures in PDF [skip ci] (5 hours ago) - commit f3769cb
  • DOC: update link to https://sylabs.io/ in usage.rst [skip ci] (6 hours ago) - commit 1f092bc
  • DOC: review indent of singularity run example [skip ci] (6 hours ago) - commit 762299c
  • DOC: update references [skip ci] (6 hours ago) - commit 323a36e
  • DOC: update runonhpc.rst [skip ci] (6 hours ago) - commit 18e797c
  • DOC: rename page for api_doc [skip ci] (6 hours ago) - commit 5405c4f
  • DOC: update runonhpc.rst [skip ci] (6 hours ago) - commit 590306e
  • Merge branch 'v3.0.0-RC2-dev' into 57_documentation_v3.0.0-RC2-dev [skip ci] (7 hours ago) - commit 2c586eb
  • DOC: update doc about singularity and datalad [skip ci] (7 hours ago) - commit eae2a37
  • DOC: update list of changes [skip ci] (7 hours ago) - commit 958065f
  • Merge pull request #56 from connectomicslab/55_singularity_v3.0.0-RC2-dev (8 hours ago) - commit f2d772a
  • MAINT: correct variable name to be PEP8 compliant (17 hours ago) - commit 4e518c1
  • FIX: rename variables correctly in cmtklib/parcellation.py and correct indent (18 hours ago) - commit 853b963
  • DOC: add docstrings and reviewed indents in run.py [skip ci] (23 hours ago) - commit a48a986
  • MAINT: review name and unused variables in cmtklib/parcellation.py (24 hours ago) - commit 22e96c2
  • FIX: config files in BIDS App GUI [skip ci] (25 hours ago) - commit e9e4449
  • FIX: mapping of config files in docker run command generated by GUI [skip ci] (25 hours ago) - commit df8728a
  • MAINT: remove unnecessary parenthesis [skip ci] (26 hours ago) - commit 71f0122
  • MAINT: code cleaning (27 hours ago) - commit 1b75da6
  • MAINT: simplify expression (27 hours ago) - commit 4663f13
  • Revert "MAINT: simplify expression" (27 hours ago) - commit ac9aed2
  • MAINT: simplify expression (27 hours ago) - commit 1ce54bd
  • FIX: correct Dipy PeakAndMetrics.shm_coeffs (27 hours ago) - commit 4f29c2d
  • DOC: correct docstring issues (27 hours ago) - commit 80b4e64
  • PEP: correct all PEP8 code style errors reported by pycharm (28 hours ago) - commit 43c18ba
  • ENH: Generate docker run command in GUI with new BIDS App options flags to control RDG and multithreading [skip ci] (30 hours ago) - commit ea7559e
  • FIX: map appropriately the configuration files in the docker run command generated by the GUI [skip ci] (31 hours ago) - commit 53c5dc7
  • ENH: added new traits in the BIDS App GUI to control RDG and multi-threading and reviewed layout [skip ci] (31 hours ago) - commit 0784728
  • Merge branch 'v3.0.0-RC2-dev' into 55_singularity_v3.0.0-RC2-dev (33 hours ago) - commit b4877b9
  • REF: review list, name, and default value of parameters for RDG and multi-threading in parser.py and run.py (33 hours ago) - commit 4538ac3
  • Merge pull request #60 from connectomicslab/reproducibility_control_v3.0.0-RC2-dev (34 hours ago) - commit d066415
  • TEST: fix name of output files (34 hours ago) - commit 3f2c618
  • CI: enable and update difference check of list of outputs for singularity tests (2 days ago) - commit c87ca63
  • TEST: updated list of outputs for singularity test (2 days ago) - commit 0e90343
  • TYPO: corrected to args.set_mkl_num_threads in run.py (2 days ago) - commit d77b4e7
  • ENH: add options to BIDS App to fix multiple envvars related to random generator seed and number of threads (2 days ago) - commit 247ed73
  • MAINT: review message when report is sent to analytics [skip ci] (2 days ago) - commit 89a75c7
  • FIX: set self.number_of_threads_max and added comments for dmri/fmri data check [skip ci] (2 days ago) - commit 574e0ae
  • DOCKER: remove build-essential after building mrtrix [skip ci] (2 days ago) - commit 0f934f6
  • CI: review order of jobs to give priority to test_singularity [skip ci] (2 days ago) - commit 3a2febc
  • ENH: display configuration of diffusion and or fmri pipeline in BIDS App Window if inputs are available [skip ci] (2 days ago) - commit 7f9d988
  • DOCKER: Remove packages for qt4 and opengl libraries as mrtrix is build with -nogui [skip ci] (2 days ago) - commit 4af790b
  • DOCKER: edit cleaning of installation step of matlab for freesurfer [skip ci] (2 days ago) - commit 422de2e
  • DOC: update comment for FSL 5 python 3 patch [skip ci] (2 days ago) - commit a49611f
  • CI: review job order/dependence for singularity build and tests (2 days ago) - commit 13f9cf3
  • DOCKER: add patch from ndmg for FSL 5.0.9 and python (2 days ago) - commit c52e4d9
  • REVERT: remove v as prefix to extracted version in build_bidsapp.sh [skip ci] (2 days ago) - commit 920d2d0
  • DOCKER: remove comment that raised an empty continuation line [skip ci] (2 days ago) - commit 57212d3
  • DOCKER: fix empty continuation line (2 days ago) - commit 625de0a
  • TYPO: add v as prefix to extracted version in build_bidsapp.sh (2 days ago) - commit 53ffc89
  • DOCKER: review cleaning of docker image and install fsl 5.0.9 much more light (2 days ago) - commit 586d643
  • DOCKER: correct paths (3 days ago) - commit cb9408b
  • DOCKER: refactoring to use only one docker file with multi-stage (3 days ago) - commit 676a6ea
  • DOCKER: removed resources from .dockerignore (3 days ago) - commit b474efb
  • CONDA: move obspy (3 days ago) - commit f68ae9c
  • DOCKER: remove bin/freeview (3 days ago) - commit ff515e1
  • DOCKER: removed lib/vtk bin/qt.conf from exclude in freesurfer (3 days ago) - commit d2708a2
  • DOCKER: exclude freeview related files when extracting freesurfer (3 days ago) - commit 6f4771a
  • DOCKER: review conda bin path (3 days ago) - commit 5c29c26
  • DOCKER: add -y to apt-get remove curl (3 days ago) - commit daf20d7
  • DOCKER: add -y to apt-get remove curl (3 days ago) - commit 3aef9b2
  • CI: revert back to use docker registry for singularity build (3 days ago) - commit 5044762
  • DOCKER: clean and try to reduce layer size (3 days ago) - commit 3caeb46
  • DOCKER: add folders to be ignored in .dockerignore (3 days ago) - commit 4b9cb3c
  • CI: review singularity build with docker-deamon and show storage information (2) (3 days ago) - commit b0ba184
  • CI: review singularity build with docker-deamon and show storage information (3 days ago) - commit d154709
  • CI: add SINGULARITY_DISABLE_CACHE=true (6 days ago) - commit 76a9dce
  • CI: add --debug -v to singularity build (6 days ago) - commit 66e4972
  • CI: try to set tmp dir environment variables directly at singularity build (6 days ago) - commit 4b934d9
  • CI: try to set TMPDIR for singularity build (6 days ago) - commit 3f65016
  • FIX: docker run command generated by GUI [skip ci] (6 days ago) - commit 54e7ba3
  • FIX: updated label for sift in configurator GUI [skip ci] (6 days ago) - commit 697a97e
  • FIX: size of image icon for quality check button in main GUI [skip ci] (6 days ago) - commit c5ef30a
  • FIX: corrected sift2 -> sift [skip ci] (6 days ago) - commit 27a61ef
  • FIX: do not resize image icons for buttons of main GUI [skip ci] (6 days ago) - commit 5aba00e
  • CI: remove /tmp/cache/docker.tar.gz in job after loading (6 days ago) - commit e6118fa
  • CI: try to set different tmp cache dir for singularity build for resolving no space left on device error (6 days ago) - commit 0bae5a7
  • Merge branch 'v3.0.0-RC2-dev' into 55_singularity_v3.0.0-RC2-dev (7 days ago) - commit aaa9d6d
  • Merge pull request #52 from connectomicslab/48_sift2_v3.0.0-RC2 (7 days ago) - commit 8e96279
  • CI: show docker images to see if possible to remove one to reduce size on disk (7 days ago) - commit ab1404d
  • DOC: update usage.rst [skip ci] (7 days ago) - commit 6da7dd9
  • DOC: update changes.rst [skip ci] (7 days ago) - commit b8a819c
  • DOC: update changes.rst [skip ci] (7 days ago) - commit 4343af7
  • DOC: add changes for version 3.0.0-RC2 [skip ci] (7 days ago) - commit 261a99a
  • DOC: add warning regarding the little tracker [skip ci] (7 days ago) - commit 5b9c9d8
  • FIX: correct indent in .circleci/config.yml (7 days ago) - commit 7239aa4
  • FIX: correct typo in .circleci/config.yml (7 days ago) - commit 68bd9f3
  • ENH: add jobs to build, test and deploy the singularity image to sylabs.io (#55) (7 days ago) - commit 46d6ff5
  • FIX: corrected code (7 days ago) - commit 37b46c5
  • TEST: updated list of outputs and re-enable diff check for tests 01 and 02 (7 days ago) - commit 7c18c83
  • MAINT: code layout (8 days ago) - commit 94236d3
  • ENH: use SIFT instead of SIFT2 to filter tractogram (8 days ago) - commit 9688410
  • FIX: add act_file input to FilterTractogram (8 days ago) - commit 2609789
  • DOC: add new sift2 config to docstring (8 days ago) - commit a30fe9c
  • REV: review rescaled images of buttons for GUI windows (8 days ago) - commit 32f18b0
  • MAINT: code cleaning and code style in cmpbidsappmanager (8 days ago) - commit fa60267
  • ADD: rescaled images of buttons for GUI windows (8 days ago) - commit 5e66c47
  • FIX: display of QPushButton for pipeline stages and the different GUI windows [skip ci] This was achieved was using a single Qt style sheet per button (see https://stackoverflow.com/questions/37058585/how-can-i-use-a-qt4-id-or-class-selector-in-the-style-sheet-with-traitsui) with the attribute border-image (see https://doc.qt.io/qt-5/stylesheet-examples.html#qpushbutton-and-images) (8 days ago) - commit dd55d89
  • Merge branch 'v3.0.0-RC2-dev' into 48_sift2_v3.0.0-RC2 (9 days ago) - commit 868c06b
  • [DOC] add docstrings and generate API docs (9 days ago) - commit dc7f831
  • ENH: changes related to the addition of the new interface for sift2 in the diffusion workflow (9 days ago) - commit 280cea8
  • DOC: update api_doc.rst [skip ci] (9 days ago) - commit 17047b7
  • REF: created entrypoint scripts in separate file as it was creating export issues for singularity (fixes #47) (9 days ago) - commit 039d353
  • DOC: review toctree depth (10 days ago) - commit bbc3d8d
  • DOC: update paths in TOCs in api_doc.rst (10 days ago) - commit e53c897
  • FIX: add missing "'" to fix EOL error (10 days ago) - commit e0ab1c5
  • DOC: updated api main file (10 days ago) - commit dd2f6be
  • DOC: add missing desc for interface input/output (12 days ago) - commit 4dc6739
  • DOC: add missing desc for interface input/output (12 days ago) - commit dd7ced7
  • DOC: add all missing input/output description for correct doc rendering (12 days ago) - commit 159378b
  • DOC: try to correct rendering of some fsl interfaces (12 days ago) - commit 3d55216
  • DOC: try to correct rendering of some fsl interfaces (12 days ago) - commit bad9d94
  • DOC: added blank lines between nipype inputs and outputs for correct doc rendering (12 days ago) - commit dacb9c2
  • DOC: update max_depth of toc in sphinx-apidoc option (12 days ago) - commit e4d55a8
  • DOC: updated spninx-apidoc options and add TOC modules (12 days ago) - commit b6d2263
  • DOC: review sphinx-apidoc build options (12 days ago) - commit 9ca7fcc
  • DEL: remove unused splitBvecVal interface in stages/preprocessing.py (12 days ago) - commit a52f094
  • DOC: fix indent in fmripipeline docstring (12 days ago) - commit bd8991d
  • DOC: reviewed get icon to return None when READTHEDOCS is detected (12 days ago) - commit ad90c5d
  • DEBUG: print icon (12 days ago) - commit b6c7992
  • FIX: try with pass (12 days ago) - commit 6623385
  • FIX: reviewed exception as it seems to not be handled (12 days ago) - commit 2c0b27f
  • FIX: move return in tray/catch of get_icon() in gui.py (12 days ago) - commit 98c6249
  • FIX: reviewed way to link image in gui.py to enable building the doc (12 days ago) - commit 163b6f1
  • DOC: try the -n sphinx option [skip ci] (13 days ago) - commit bcad2e2
  • DOC: update requirements and autodoc_mock_import [skip ci] (13 days ago) - commit d94e084
  • DOC: add traitsui to autodoc_mock_imports [skip ci] (13 days ago) - commit 9e6046c
  • DOC: add pyface to autodoc_mock_imports [skip ci] (13 days ago) - commit 6a1b3b0
  • DOC: add PySide2 to autodoc_mock_imports [skip ci] (13 days ago) - commit e49bc13
  • DOC: use PySide2 (13 days ago) - commit 3952764
  • DOC: use pyface (13 days ago) - commit 04c553a
  • FIX: import traits in cmtklib/diffusion.py (13 days ago) - commit 8d495b6
  • DOC: corrected imports and review how to handle dipy [skip ci] (13 days ago) - commit 2d4a33b
  • DOC: update versions in requirements.txt [skip ci] (13 days ago) - commit 3f54c27
  • GIT: ignore new generated api documentation files (13 days ago) - commit d08edc5
  • DOC: review rewuirements.txt and autodoc_mock_imports [skip ci] (13 days ago) - commit 9f26984
  • DOC: add pyface to autodoc_mock_imports (13 days ago) - commit 6e49281
  • DOC: try an other way to access cmp on path for autodoc (13 days ago) - commit 8164d3d
  • DOC: try an other way to access cmp on path for autodoc (13 days ago) - commit 4ac6018
  • DOC: try an other way to access cmp on path for autodoc (13 days ago) - commit 6318337
  • DOC: fix path to module cmp (13 days ago) - commit cb0f1c0
  • DOC: removed numpy from autodoc_mock_imports (13 days ago) - commit 8f1d773
  • DOC: add matplotlib in requirements.txt [skip ci] (13 days ago) - commit bf92d18
  • DOC: test API doc on readthedocs (13 days ago) - commit 0288ff7
  • DOC: add docstrings in cmtklib/bids/utils.py (13 days ago) - commit b04e657
  • DOC: add docstrings in cmtklib/interfaces/mrtrix3.py (13 days ago) - commit f5786be
  • DOC: corrected typo in docstring example (13 days ago) - commit f4f03fe
  • MAINT: add new line at end of files (13 days ago) - commit 3de0ec6
  • REF: Move interfaces from misc to cmtklib/diffusion (13 days ago) - commit 36ffd50
  • REF: rename class name with capital letter in interfaces/misc.py (13 days ago) - commit 8a4151b
  • REF: rename class name with capital letter (13 days ago) - commit 5660794
  • REF: Move interfaces from misc to fsl (13 days ago) - commit dc7f344
  • DOC: add docstrings to cmtklib/interfaces/misc.py (13 days ago) - commit 04c759d
  • DOC: started to add docstring in interfaces/misc.py (2 weeks ago) - commit d356dd0
  • DEL: removed unused interface match_orientation (2 weeks ago) - commit 3c4e737
  • DEL: remove CMP2 interfaces to MITK (2 weeks ago) - commit fa3f939
  • MAINT: update docstring and clean code in cmtklib/interfaces/fsl.py (2 weeks ago) - commit 913111c
  • DOC: update docstrings in cmtklib/freesurfer.py (2 weeks ago) - commit 87306a3
  • DOC: update docstrings in cmtklib/dipy.py (2 weeks ago) - commit 1ba05e7
  • DOC: update docstrings in cmtklib/diffusion_toolkit.py (2 weeks ago) - commit 0448148
  • DOC: update docstrings in cmtklib/camino2trackvis.py (2 weeks ago) - commit 59be836
  • DOC: update docstrings in cmtklib/camino.py (2 weeks ago) - commit 68e03cb
  • DOC: update docstrings in cmtklib/ants.py (2 weeks ago) - commit db5d030
  • DOC: update docstrings in cmtklib/afni.py (2 weeks ago) - commit 1d2bd6e
  • DOC: add docstrings in cmtklib/parcellation.py (2 weeks ago) - commit 80c7152
  • MAINT: add capital letter for classes in cmtklib/functionalMRI.py (2 weeks ago) - commit 2c92437
  • DOC: added docstrings in cmtklib/functionalMRI.py (2 weeks ago) - commit 861e30e
  • DOC: corrected examples in docstrings of connectome.py (2 weeks ago) - commit 59c869e
  • DOC: add docstrings in cmtklib/diffusion.py [skip ci] (2 weeks ago) - commit 3c1b3ca
  • DOC: add docstrings in cmtklib/connectome.py [skip ci] (2 weeks ago) - commit 0d63ead
  • DOC: add docstring in cmtklib/config.py (2 weeks ago) - commit b0cf724
  • MAINT: use capital letter for class BColors (2 weeks ago) - commit 3de621e
  • DOC: add docstrings in cmtklib/utils.py (2 weeks ago) - commit 49c3fdc
  • DOC: update attributes/param syntax in stages of bidsappmanager [skip ci] (5 weeks ago) - commit 35c25dc
  • DOC: update attributes/param syntax in bidsappmanager/core.py [skip ci] (5 weeks ago) - commit 8714b0c
  • DOC: update attributes/param syntax in main and pipeline files of bidsappmanager [skip ci] (5 weeks ago) - commit 1160861
  • DOC: add module docstring to cmp/viz/reports.py [skip ci] (5 weeks ago) - commit 0c42cb9
  • MAINT: removed binaries related to the Diffusion Toolkit (DTK) [skip ci] (5 weeks ago) - commit d9c7c9b
  • DOC: add docstrings to cmp/project.py [skip ci] (5 weeks ago) - commit d28fa5d
  • DOC: review docstrings in pipelines/common.py [skip ci] (5 weeks ago) - commit a82e1d2
  • DOC: add docstring in stages/common.py [skip ci] (5 weeks ago) - commit 83da602
  • FIX: correct project_info.subject_session in anatomical.py and review code layout in all pipelines (5 weeks ago) - commit 74fa328
  • DOC: add docstrings to segmentation.py [skip ci] (5 weeks ago) - commit 6204f1f
  • DOC: add docstrings to registration.py [skip ci] (5 weeks ago) - commit 0e6055e
  • DOC: complete docstrings to preprocessing.py [skip ci] (5 weeks ago) - commit 7f1a245
  • DOC: add docstrings to parcellation.py [skip ci] (5 weeks ago) - commit 074a88b
  • DOC: add create_workflow() as Methods to stage class docstring [skip ci] (5 weeks ago) - commit 23d7aff
  • DOC: add create_workflow() as Methods to stage class docstrings [skip ci] (5 weeks ago) - commit e9bacfd
  • DOC: modify docstring of constructor [skip ci] (5 weeks ago) - commit 5b823a3
  • DOC: add docstrings in preprocessing.py [skip ci] (5 weeks ago) - commit 864bdd3
  • DOC: fix typo in connectome.py and fmri_connectome.py [skip ci] (5 weeks ago) - commit a9e9fec
  • FIX: reviewed constructors of pipelines (5 weeks ago) - commit d005f71
  • DOC: add docstring to frmi_preprocessing.py [skip ci] (5 weeks ago) - commit 3bebb98
  • DOC: add docstrings to parcellation.py [skip ci] (5 weeks ago) - commit b2096e8
  • DOC: correct typo in docstring of functionalMRI.py [skip ci] (5 weeks ago) - commit 4c09ca0
  • MAINT: removed extra parenthesis (6 weeks ago) - commit ef787a8
  • DOC: add missing docstrings in constructors (6 weeks ago) - commit 7349b1a
  • DOC: Add docstring to functionalMRI.py (6 weeks ago) - commit 0ea81e1
  • DOC: added docstrings to connectome and diffusion stages (6 weeks ago) - commit 3714180
  • DOC: update doctring modules in cmp.bidsappmanager.pipelines and cmp.bidsappmanager.stages [skip ci] (6 weeks ago) - commit 8b887ce
  • DOC: add docstrings in fMRI.py (6 weeks ago) - commit 49719ef
  • DOC: add docstring to GLobalConfigurations class [skip ci] (6 weeks ago) - commit b03f47b
  • DOC: correct parameter type description in docstring [skip ci] (6 weeks ago) - commit 01ef32c
  • DOC: update and missing doctrings [skip ci] (6 weeks ago) - commit df75aa9
  • DOC: add empty docstring generated by pycharm (6 weeks ago) - commit ef75d0a
  • DOC: reviewed doctrings with info on inheritance (6 weeks ago) - commit 20cc7ca
  • DOC: added docstrings and cleaning in gui.py and project.py (cmp.bidsappmanager) (6 weeks ago) - commit 4277d44
  • FIX: install cmtklib.bids (7 weeks ago) - commit cb88a97
  • DOC: started docstring in cmp.project [skip ci] (7 weeks ago) - commit adcd301
  • DOC: add docstring to bidsappmanager.core [skip ci] (7 weeks ago) - commit 04ebd39
  • REF: refactored project_info and started docstring in bidsappmanager.gui [skip ci] (7 weeks ago) - commit 453dd2b
  • MAINT: renamed classes and replaced CMP_MainWindow by CMP_MainWindowV2 (7 weeks ago) - commit 1bced8d
  • MAINT: cleaning for cmpbidsappmanager.project.py [skip ci] (7 weeks ago) - commit 1bddbe5
  • DOC: add docstrings to cmpbidsappmanager pipeline and stage files (7 weeks ago) - commit c43f0a8
  • FIX: add dc package to be installed inside the container to make BET happy (see #50) (7 weeks ago) - commit 95c26e3
  • FIX: removed the extra installation of bc along fsl as it seems to be installed inside the container (see #50) (7 weeks ago) - commit ade8a45
  • FIX: dc should be indeed part of bc package that is now install along with FSL to make BET happy (see #50) (7 weeks ago) - commit 5fe1125
  • FIX: add dc package to be installed inside the container to make BET happy (see #50) (7 weeks ago) - commit 163bdf8
  • DOC: add link to contributing page and add section tile for contribution types (7 weeks ago) - commit cbb4a51
  • DOC: update readthedocs config to install cmp (7 weeks ago) - commit 276b355
  • DOC: update readthedocs config to install cmp (7 weeks ago) - commit 7989c7c
  • DOC: update readthedocs config to install cmp (7 weeks ago) - commit bb5fde5
  • DOC: fix typo for warning box (7 weeks ago) - commit 72cec74
  • DOC: update readthedocs YAML config file to V2 (7 weeks ago) - commit 7876333
  • Git: ignore .idea/ folders (7 weeks ago) - commit 2a64fbf
  • DOC: update instructions for contributions (7 weeks ago) - commit 6e42383
  • DOC: add warning about tracking system and how to opt-out (7 weeks ago) - commit 7066c3e
  • ENH: add a tracking system to report usage system (7 weeks ago) - commit 1f8636d
  • VERSION: update to v3.0.0-RC2 (3 months ago) - commit 6f206bd
  • FIX: install missing package dependencies (cvxpy and cvxpy-base) of mapmri (3 months ago) - commit 8bdfca6
  • MAINT: remove option to normalize dwi to B0 for mrtrix3 csd (3 months ago) - commit 79dbf0f
  • MAINT: correct code style issues (3 months ago) - commit 2330e7e
  • ENH: add option to specify number of threads in BIDS App interface GUI (3 months ago) - commit 19044e4
  • ENH: add option to change output directory of BIDS App Interface GUI (3 months ago) - commit 1a284c0
  • FIX: correct conditions for running anat/dwi/func pipelines with coverage (3 months ago) - commit 76b410d
  • CI: add test processing anatomical + fmri pipelines (3 months ago) - commit 507e4a7
  • FIX: renamed appropriately variable of dipy_recon_config_ui for GUI (3 months ago) - commit 69d50b8
  • FIX: convert number_of_threads to string type (3 months ago) - commit da16620
  • DOC: update instructions for installation (Python 3) [skip ci] (4 months ago) - commit a12ce93

Auto-generated with

git log v3.0.0-RC1 --pretty=format:' * %s %Cgreen(%cr) - commit %Cred%h%Creset' --abbrev-commit
e3d1554
Compare
Choose a tag to compare

This is the first release candidate v3.0.0-RC1 of the Connectome Mapper which merges PR #40.

Summary of changes is available at the documentation.

Complete list of changes with respect to previous 3.0.0-beta-RC2:

  • Merge pull request #40 from connectomicslab/python3 (10 minutes ago) - commit 4e9d6e5
  • MAINT: deleted useless commented section (10 days ago) - commit e336dd8
  • DOC: update index and readme pages with codacy badges [skip ci] (10 days ago) - commit 6b64f8d
  • MAINT: commented assert [skip ci] (10 days ago) - commit 71ca362
  • MAINT: removed (last hopefully :) ) unused imports and variables and PEP8 errors [skip ci] (10 days ago) - commit be88f81
  • MAINT: removed a number of additional unused imports and fixed additional PEP8 errors (10 days ago) - commit 0fa93f1
  • CI: update list outputs for test 01 and test 02 following change in test 01 (ANTs -> FLIRT registration) (10 days ago) - commit 0fd6696
  • MAINT: corrected a number of additional code style issues and un-used imports (11 days ago) - commit a979ef9
  • MAINT: corrected a number of additional code style issues and un-used imports (11 days ago) - commit 15ce5e5
  • MAINT: corrected a number of additional code style issues and un-used imports (11 days ago) - commit b7dd376
  • MAINT: corrected a number of code style issues and un-used imports [skip ci] (11 days ago) - commit 3e8ed0d
  • MAINT: update copyright year (11 days ago) - commit d0ac87d
  • CI: comment lines for checking outputs of test-01 as outputs changed (FLIRT instead of ANTs SyN registration) (11 days ago) - commit dc9d690
  • FIX: correct duplicate node name in registration stage using FSL FLIRT (11 days ago) - commit 0ddcaa2
  • DOC: reviewed list of dependency upgrades [skip ci] (11 days ago) - commit e349e5e
  • DOC: updated list of dependency upgrades in list of changes [skip ci] (11 days ago) - commit d2889a6
  • DOC: update link to codacy project page of CMP3 [skip ci] (11 days ago) - commit c8e450d
  • DOC: updated list of changes [skip ci] (11 days ago) - commit 4730656
  • DOC: updated list of changes [skip ci] (11 days ago) - commit 52ea379
  • MAINT: split long string over extra line (11 days ago) - commit badb766
  • CI: tracks files for tests in the new folders and update using FSL FLIRT in test 1 for improved coverage of registration (11 days ago) - commit 2fbc749
  • CI: rearranged folder/file structure for configs + lists of outputs of tests in circleci (11 days ago) - commit 50c359c
  • FIX: convert number_of_threads to str for OMP_NUM_THREADS (12 days ago) - commit 5f606b3
  • MAINT: better handle the number of max cores to use (12 days ago) - commit c1b88d6
  • ENH: implemented option to specify number of parallel threads used by Freesurfer and ANTs at segmentation stage and by Softwares based on OpenMP (12 days ago) - commit 5acf82e
  • ENH: add option in GUI to specify the number of parallel threads used by OpenMP in Freesurfer and ANTs (12 days ago) - commit de27e34
  • CI: improve coverage by running define_inspect_outputs() for each stage (12 days ago) - commit c292788
  • DOC: updated list of changes for this version (13 days ago) - commit abc9bdd
  • DOC: updated label for atlas in outputs doc (13 days ago) - commit ae4e1bf
  • MAINT: deleted obsolete files [skip ci] (13 days ago) - commit 563deb4
  • DOC: updated index and readme descriptions (13 days ago) - commit 778d9b7
  • CI: updated/enabled check of list of outputs for test_parcellation job (13 days ago) - commit 78a3da2
  • FIX: get graphml filename for computing roi volumetry in Lausanne2008 parcellation (2 weeks ago) - commit 6efbf3c
  • CI: uncomment missing job depencies of covergae report job (2 weeks ago) - commit ee4581e
  • CI: new attempt to make the test_parcellation job not performing again recon-all (2 weeks ago) - commit ff1487b
  • MAINT: update version (2 weeks ago) - commit 468a43e
  • CI. reviee how to save / load test_dsi_dipy derivatives to test other parcellations (2 weeks ago) - commit 2672538
  • DOC: added preview png for ohbm poster 2020 [skip ci] (2 weeks ago) - commit b8732c4
  • DOC: reviewed how to cite connectomemapper3 [skip ci] (2 weeks ago) - commit 0eff9d4
  • DOC: changed badge style for circleci status [skip ci] (2 weeks ago) - commit 6eabf8e
  • ZENODO: removed publication date (2 weeks ago) - commit a01031a
  • CI: re-enable check of differences between list of outputs in pipeline execution tests 01->04 (2 weeks ago) - commit f813653
  • CI: update output list for dipy prob tracking (2 weeks ago) - commit 2eb92d8
  • CI: check if way to reduce time of test_parcellation (2nd try) (2 weeks ago) - commit 3242528
  • CI: check if way to reduce time of test_parcellation (3 weeks ago) - commit a5c7961
  • CI: updated list of outputs and should correct test dipy prob tracking (3 weeks ago) - commit df4cdd7
  • CI: commented job for testing other parcellation schemes (3 weeks ago) - commit 67228bc
  • CI: hard code paths in store_artifacts (use of environment variable there seems not working) (3 weeks ago) - commit c853bcd
  • DOC: updated list of changes related to this release [skip ci] (4 weeks ago) - commit 616f4bd
  • MAINT: commented all CMP2-inherited parts that give the user the possibility its own custom segmentation / parcellation / diffusion FODFs / tractograms (4 weeks ago) - commit 16955b5
  • MAINT: clean prints and add comment to cmat function that computes structural connectivity matrices [skip ci] (4 weeks ago) - commit 5376de3
  • CI: fix paths to check outputs and create the file list following the refactoring in previous commit (4 weeks ago) - commit aa54088
  • CI: create a ds-sample dataset dedicated to each test job and correct handling of skipping test jobs in commit message (4 weeks ago) - commit b5785e4
  • FIX: missing renamed roi_graphmls input to cmtk_cmat interface (4 weeks ago) - commit 40389c2
  • FIX: renaming SHORE lambdas variable (not MixedCase) (4 weeks ago) - commit 4eadf05
  • CI: fix typo in workspace path for tests (4 weeks ago) - commit 5d1ad0b
  • MAINT: fix mixedCase code style issues [skip ci] (4 weeks ago) - commit 30c5a42
  • MAINT: fix code style issues [skip ci] (4 weeks ago) - commit 99323dc
  • MAINT: correct code style issues [skip ci] (4 weeks ago) - commit 14d6ea0
  • README: fix code style issue [skip ci] (4 weeks ago) - commit 64a8b6f
  • CI: reviewed job dependencies (4 weeks ago) - commit 3ea85de
  • CI: split test job in multiple jobs (5h hard limit imposed by CircleCI) (4 weeks ago) - commit 4fbc923
  • DOC: update changes (4 weeks ago) - commit ca7d1ea
  • MAINT: review how to save tractogram (Dipy 1.0 changes) (4 weeks ago) - commit aaa476e
  • FIX: create mask to compute peaks from Dipy CSD (4 weeks ago) - commit 05ad404
  • FIX: correct paths to Lausanne2008 graphml node description files (4 weeks ago) - commit 2f6c3dd
  • FIX: correct model in maps generated by dipy tensor fit (4 weeks ago) - commit 9bb6cce
  • FIX: rename maps generated by dipy CSD (4 weeks ago) - commit 07561b8
  • FIX: rename ouput volumetry file for NativeFreesurfer parcellation scheme (4 weeks ago) - commit f15b7e8
  • MAINT: updated imports to save tractograms with Dipy (Dipy 1.0 API changes) (4 weeks ago) - commit ec75602
  • MAINT: updated code to save tractograms with Dipy (Dipy 1.0 API changes) (4 weeks ago) - commit 56e36ac
  • MAINT: clean code for SHORE interface (4 weeks ago) - commit 5e73a7a
  • MAINT: review how to import peaks_from_model (Dipy 1.0 API changes) (4 weeks ago) - commit e1dfe68
  • MAINT: renamed *TissueClassifier -> *StoppingCriterion (Dipy 1.0 changes) (4 weeks ago) - commit 642b0d3
  • MAINT: fix import changes with Dipy 1.0 (4 weeks ago) - commit 0db0133
  • CI: commented diff of lists of output files (4 weeks ago) - commit 8670d4f
  • DOC: minor changes in homepage [skip ci] (4 weeks ago) - commit 957895f
  • DOC: add OHBM citation and reviewed display of citation and refs (4 weeks ago) - commit cf0eee6
  • DOC: correct typo (4 weeks ago) - commit 6f34511
  • ENH: started implementation of json config files (4 weeks ago) - commit 0dc7dec
  • CI: reviewed how to save log in circleci when coverage run is used (4 weeks ago) - commit 0526848
  • FIX: calls to nibabel modules (4 weeks ago) - commit 2d790d4
  • FIX: correct shm basis used in dipy shore (5 weeks ago) - commit 3b5f678
  • DOC: correct badge text for docker version [skip ci] (5 weeks ago) - commit b560c6c
  • DOC: update home page [skip ci] (5 weeks ago) - commit c58e32c
  • DOC: update to recently released BIDS v1.4 [skip ci] (5 weeks ago) - commit 4a2c229
  • DOC: add description of output graph filenames (5 weeks ago) - commit 96c911d
  • DOC: correct typo (5 weeks ago) - commit ea511fd
  • DOC: update home page (5 weeks ago) - commit e054a28
  • DOC: started description of changes for this upcoming version [skip ci] (5 weeks ago) - commit 31372e5
  • Update README.md (5 weeks ago) - commit 51133d9
  • Update README.md (5 weeks ago) - commit e432c6a
  • FIX: better handle config file args for coverage in circleci (5 weeks ago) - commit 79bd336
  • FIX: better handle config file args for coverage in circleci (5 weeks ago) - commit dcea895
  • MAINT: update command for coverage (5 weeks ago) - commit 8220ea1
  • MAINT: clean printouts (5 weeks ago) - commit 2167a76
  • FIX: update mne code for circular layout code (5 weeks ago) - commit 4579330
  • FIX: update mne code for circular layout plot (5 weeks ago) - commit 6610dcc
  • FIX: compute connectivity matrices (5 weeks ago) - commit f144d5c
  • FIX: add condition for change in attributes name of nodes in graphml (5 weeks ago) - commit f5a0cae
  • FIX: wrong filename (5 weeks ago) - commit 92e4a6e
  • FIX: wrong output for other parcellation scheme to compute roi volumetry (5 weeks ago) - commit 61ae00a
  • FIX: removed extra arg (5 weeks ago) - commit b886c56
  • FIX: add other parcellation schemes to interface that compute roi volumetry (5 weeks ago) - commit a53698b
  • ENH: re factored code for better coverage of CI test runs (5 weeks ago) - commit 2ecc8c2
  • MAINT: replace env by variable (5 weeks ago) - commit 6a208bd
  • CI: rename log file of multiple test runs (otherwise they are overwritten) (5 weeks ago) - commit c52a6af
  • ENH: add coverage option in BIDS App options for circleci (5 weeks ago) - commit 33b9211
  • CI: fix space in filenames (5 weeks ago) - commit c2ee186
  • ENH: save FC matrices as TSV files (5 weeks ago) - commit ccd3859
  • CI: updated source modules for coverage (5 weeks ago) - commit 69d3a58
  • ENH: write structural connectivity matrices as TSV files (5 weeks ago) - commit da898c0
  • FIX: inspect outputs of fmri pipeline (5 weeks ago) - commit 31e9afc
  • CI: specified new source packages for coverage (5 weeks ago) - commit 4340ade
  • CI: fix regression tests and generation of output lists (5 weeks ago) - commit e73d6fd
  • CI: fix indent (5 weeks ago) - commit 325486f
  • CI: add more regression tests with different config (5 weeks ago) - commit 54006d0
  • Update config.yml (5 weeks ago) - commit aeba7d5
  • CI: make coverage persist in workspace (5 weeks ago) - commit cb5d4ce
  • CI: remove line "run command..." causing error (6 weeks ago) - commit 6df0fe6
  • CI: fix indent (6 weeks ago) - commit 06c6561
  • Update ds-sample_outputs.txt (6 weeks ago) - commit 26cb0f1
  • CI: add independent job for sending coverage report to codacy (6 weeks ago) - commit 216542c
  • FIX: remove copy of missing .coveragrc file (6 weeks ago) - commit dc14778
  • Update config.yml (6 weeks ago) - commit 44b1a81
  • Update config.yml (6 weeks ago) - commit b28950e
  • CI: update coverage to codacy (6 weeks ago) - commit 928e692
  • ENH. omit files for GUI in coverage (6 weeks ago) - commit 4c06fb3
  • FIX: add missing && in installation of mrtrix3 (6 weeks ago) - commit 2bdf958
  • FIX: remove extra RUn to create conda env (6 weeks ago) - commit 7e087a3
  • CI: update with coverage run and report (6 weeks ago) - commit 9692872
  • MAINT: fix double quote issue (6 weeks ago) - commit 27392e4
  • MAINT: ignore git related files in docker (6 weeks ago) - commit 13557b5
  • CI: remove main docker image for sake of storage on circleci (6 weeks ago) - commit fa220d8
  • MAINT; refactored dockerfile with better cleaning (6 weeks ago) - commit d6fd514
  • MAINT: fix pep8 error with regex (6 weeks ago) - commit e1355c4
  • CI: print storage info for debugging (6 weeks ago) - commit 1b5985e
  • ENH: add example of bidsapp execution with coverage (6 weeks ago) - commit 461d54e
  • MAINT: fix codacy issues (6 weeks ago) - commit 684ebe3
  • ENH: add coverage (6 weeks ago) - commit b9be338
  • CI: rm=true in docker build (6 weeks ago) - commit a5e55b8
  • CI: try to make some space (6 weeks ago) - commit 19ec2bb
  • CI: corrected typo introduced in latest commit (7 weeks ago) - commit ae67671
  • CI: should fix the no space left on device issue (7 weeks ago) - commit b762920
  • CI: fix docker image build (7 weeks ago) - commit 0adb46a
  • DOC: maintenance (7 weeks ago) - commit 95d800d
  • MAINT: fix unused imports (7 weeks ago) - commit f6ffd8d
  • MAINT: show registration tool in fmri registration for debugging (7 weeks ago) - commit 03af119
  • FIX: inpsect output of preprocessing stage with glob (7 weeks ago) - commit 5db8055
  • MAINT: update readme (7 weeks ago) - commit 4354d61
  • MAINT: should fix codacy item/bullet related issue (7 weeks ago) - commit 16e5080
  • FIX: missing self arg in meethods to save config files (7 weeks ago) - commit a066bcc
  • FIX: formatting of entrypoint script content (7 weeks ago) - commit 0dfbc20
  • FIX: formatting of entrypoint script content (7 weeks ago) - commit 6cd4014
  • FIX: installation of missing binary calculator (bc) required by freesurfer (7 weeks ago) - commit a909b18
  • FIX: missing self arg in classmethods (7 weeks ago) - commit 1983fb9
  • MAINT: fix indent of bullets (7 weeks ago) - commit 9d70dbe
  • MAINT: fix "except:" codacy issues (7 weeks ago) - commit b514acc
  • MAINT: fixed codacy errors in all grade F files (7 weeks ago) - commit 0e05a9a
  • MAINT: fix codacy issues in anatomical.py and correct is True and is False (7 weeks ago) - commit 071c411
  • MAINT: fix trailing whitespace with sublimetext save (7 weeks ago) - commit 08a9bf2
  • MAINT: fix codacy code style error (7 weeks ago) - commit f9bea93
  • MAINT: fix codacy code style errors (7 weeks ago) - commit cb88f06
  • MAINT: refactored insüect_output function that failed after migration to python 3 an multiple fixes (7 weeks ago) - commit e71b125
  • FIX: upgrade to FSL6 to solve the python2 error (7 weeks ago) - commit cd20de9
  • FIX: reviewed iteration over graph edges causing error returning non unique edges!! (8 weeks ago) - commit f57846c
  • ENH. remaining code changes in GUI related to major changes in the way we fix output path extracted from node results pickle file (8 weeks ago) - commit 2403beb
  • FIX: corrected indentation error (8 weeks ago) - commit 196a483
  • ENH: removed duplicated processing steps/code and use char type and mask for computing the dilated ventricule image (8 weeks ago) - commit 555a760
  • FIX: reviewed way we access to output of nodes and correct for bidsapp/local path Do no rewrite anymore the node pickle files with gzip as it causing Nipype trouble to read them after migration to Python 3 (8 weeks ago) - commit 2d81299
  • ENH: control dipy SH basis type for CSD (tournier and descoteaux) (8 weeks ago) - commit 8fb8995
  • FIX: corrections for configparser and code refactoring to eliminate code duplication (8 weeks ago) - commit 6e7cbac
  • WIP on python3: 1479882 FIX: correct issues raised by codacy (8 weeks ago) - commit d834717
  • index on python3: 1479882 FIX: correct issues raised by codacy (8 weeks ago) - commit dfa9788
  • FIX: correct issues raised by codacy (8 weeks ago) - commit 1479882
  • MAINT: reviewed code for creating entrypoint script to fix code style issue (8 weeks ago) - commit a5ce13c
  • FIX: Changed encoding for reading and writing pickles (BIDSApp with GUI fails to rerun) (8 weeks ago) - commit bb5a917
  • FIC: correct long line related to codacy code style issue (8 weeks ago) - commit 5b9a922
  • MAINT: renamed name of conda envs to py37... (8 weeks ago) - commit c5a1da9
  • FIX: make comments pep8 compliant (8 weeks ago) - commit ecb50d5
  • FIX: replaced remaining call to file() function (8 weeks ago) - commit d5e909a
  • FIX: removed file( function not existing in python3) (8 weeks ago) - commit b2f02ab
  • MAINT: correct some code style issues reported by codacy (8 weeks ago) - commit ea6a27a
  • FIX: TypeError: slice indices must be integers or None or have an index method (8 weeks ago) - commit 7e97511
  • MAINT: update output of connectivity matrices to ne inline with see BIDS connectivity scheme draft: https://docs.google.com/document/d/1ugBdUF6dhElXdj3u9vw0iWjE6f_Bibsro3ah7sRV0GA/edit#) (8 weeks ago) - commit 0b25f25
  • ENH: update to python 3.7 in the gui environment (8 weeks ago) - commit 0b6d33c
  • FIX: name "os" is not defined error when processing hippo/thal/brainstem... (8 weeks ago) - commit b90df55
  • ENH: update to python 3.7 (8 weeks ago) - commit a3a8ad1
  • MAINT: code cleaning (8 weeks ago) - commit 827de10
  • Related to dipy.viz (9 weeks ago) - commit ec7a41a
  • Commented part which uses dipy.viz for odf as could not find a correct set of version and packages that work together (9 weeks ago) - commit 37e04c3
  • For debug (9 weeks ago) - commit b52582f
  • FIX: specify encoding when read and save interface pickles (9 weeks ago) - commit 0c85444
  • FIX: change string.replace() -> str.replace() (9 weeks ago) - commit 28fb462
  • FIX. correct error when assigning None to freesurfer home directory (9 weeks ago) - commit 09f121e
  • FIX: return type of extractvoxeldims interface (9 weeks ago) - commit ef2021f
  • ENH: use apt-fast to install ubuntu packages and libraries (9 weeks ago) - commit a709c2d
  • FIX: corrected versions of packages installed in conda environment that now install well (9 weeks ago) - commit 7bef46a
  • FIX: update import of Nipype functions that have been moved in newer releases (9 weeks ago) - commit 7a91b0f
  • MAINT: Update dockerfile with new environment file and miniconda3 (9 weeks ago) - commit 8d45619
  • MAINT: update conda environment files to python3 (9 weeks ago) - commit 607cbdd
  • MAINT: replaced all original files with its 2to3-, pep8- corrected version (9 weeks ago) - commit baf6246
  • -MAINT: do not ignore python3 folder content in git (9 weeks ago) - commit 1f373c6
  • MAINT: fix pep8 violations with autopep8 (9 weeks ago) - commit 8564040
  • Code converted to python3 with 2to3 (9 weeks ago) - commit ea359cc
  • MAINT: missing prints (9 weeks ago) - commit 0ce4b9f
  • MAINT: reshaped parser code (9 weeks ago) - commit 49340ce
  • MAINT: fix print for python3 (9 weeks ago) - commit 424f5f8
  • DOC: reviewed docker pull badge order (9 weeks ago) - commit a4730da
  • DOC: added new badges (9 weeks ago) - commit 5a6e627
  • DOC: update circleci badge (9 weeks ago) - commit 629cc32
  • DOC: added version badge (9 weeks ago) - commit 7e5a732
  • DOC: fix layout badge (9 weeks ago) - commit 45bce9f
  • DOC: Added badge for docker pulls (9 weeks ago) - commit 06bb807
  • Remove atom config file (9 weeks ago) - commit 50d9c75

Auto-generated with

git log v3.0.0-beta-RC2..HEAD --pretty=format:' * %s %Cgreen(%cr) - commit %Cred%h%Creset' --abbrev-commit