connectomicslab/connectomemapper3: Connectome Mapper v3.0.0-RC1

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

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