Connectome Mapper v3.0.0-RC4

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

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