Connectome Mapper v3.0.0-RC3

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.