Release notes for DIPY version 1.1#

GitHub stats for 2019/08/06 - 2020/01/10 (tag: 1.0.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 11 authors contributed 392 commits.

  • Ariel Rokem

  • Derek Pisner

  • Eleftherios Garyfallidis

  • Eric Larson

  • Francois Rheault

  • Jon Haitz Legarreta Gorroño

  • Rafael Neto Henriques

  • Ricci Woo

  • Ross Lawrence

  • Serge Koudoro

  • Shreyas Fadnavis

We closed a total of 130 issues, 52 pull requests and 81 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (52):

  • PR #2030: [MAINT] Release 1.1.1

  • PR #2029: Use the array proxy instead of get_fdata()

  • PR #2023: [Upcoming] Release 1.1.0

  • PR #2021: Examples update

  • PR #2005: [CI] add python3.8 matrix

  • PR #2009: Upgrade on DKI implementations

  • PR #2022: Update pep8speaks configuration

  • PR #2020: Update get_fnames

  • PR #2018: The Python is dead. Long live the Python

  • PR #2017: Update CONTRIBUTING.md

  • PR #2016: replace get_fdata by load_nifti_data

  • PR #2012: Add ability to analyze entire streamline in connectivity_matrix

  • PR #2015: Update nibabel minimum version (3.0.0)

  • PR #1984: Enabling TensorFlow 2 as an optional dependency

  • PR #2013: SFT constructor from another SFT

  • PR #1862: Use logging instead of print statements

  • PR #1952: Adding lpca, mppca and gibbs ringing workflows

  • PR #1997: [FIX] Avoid copy of Streamlines data

  • PR #2008: Fix origin nomenclature sft (center/corner)

  • PR #1965: Horizon updates b1

  • PR #2011: BF: Use the sklearn.base interface, instead of deprecated sklearn.linear_model.base

  • PR #2002: BUG: Fix workflows IO FetchFlow all dataset fetching

  • PR #2000: NF: SplitFlow

  • PR #1999: add cenir_multib to dipy_fetch workflows

  • PR #1998: [DOC] Workflows Tutorial

  • PR #1988: DOC: Multi-Shell Multi-Tissue CSD Example

  • PR #1975: Azure CI

  • PR #1994: MAINT: Update gradient for SciPy deprecation

  • PR #1711: ENH: Improve the point distribution algorithm over the sphere.

  • PR #1989: DOC: Fix parameter docstring in dipy.io.streamline.load_tractogram

  • PR #1987: BF: use MAM distance when that is requested.

  • PR #1986: Fix the random state for SLR and Recobundles in bundle_extraction.

  • PR #1977: Add a warning on attempted import.

  • PR #1983: [Fix] one example

  • PR #1981: DOC: Improve the doc/examples/README file contents

  • PR #1980: DOC: Improve the doc/README file contents

  • PR #1978: DOC: Add extension to doc/examples/README file

  • PR #1979: DOC: Change the doc/README file extension to lowercase

  • PR #1972: Small fix in warning message

  • PR #1956: stateful_tractogram_post_1.0_fixes

  • PR #1971: fix broken link of devel

  • PR #1970: DOC: Fix typos

  • PR #1929: ENH: Relocate the sim_response method to allow reuse

  • PR #1966: ENH: Speed up Cython, remove warnings

  • PR #1967: ENH: Use language level 3

  • PR #1962: DOC: Display master branch AppVeyor status

  • PR #1961: STYLE: Remove unused import statements

  • PR #1963: DOC: Fix parameter docstring in LiFE tracking script

  • PR #1900: ENH: Add streamline deformation example and workflow

  • PR #1948: Minor Fix for Cross-Validation Example

  • PR #1951: [FIX] update some utilities scripts

  • PR #1958: Adding Missing References in SHORE docs

Issues (81):

  • #2021: Examples update

  • #2005: [CI] add python3.8 matrix

  • #1197: Documentation improvements

  • #1959: DIPY open lab meetings – fall 2019

  • #2003: Artefacts in DKI reconstruction

  • #2009: Upgrade on DKI implementations

  • #2022: Update pep8speaks configuration

  • #2020: Update get_fnames

  • #1777: Maybe read_* should return full paths?

  • #1634: Use logging instead of print statements

  • #2018: The Python is dead. Long live the Python

  • #2017: Update CONTRIBUTING.md

  • #1949: Update Horizon

  • #2016: replace get_fdata by load_nifti_data

  • #2012: Add ability to analyze entire streamline in connectivity_matrix

  • #2015: Update nibabel minimum version (3.0.0)

  • #2006: get_data deprecated

  • #1984: Enabling TensorFlow 2 as an optional dependency

  • #2013: SFT constructor from another SFT

  • #1862: Use logging instead of print statements

  • #1952: Adding lpca, mppca and gibbs ringing workflows

  • #1997: [FIX] Avoid copy of Streamlines data

  • #2014: Removes the appveyor configuration file.

  • #2008: Fix origin nomenclature sft (center/corner)

  • #1965: Horizon updates b1

  • #2011: BF: Use the sklearn.base interface, instead of deprecated sklearn.linear_model.base

  • #2010: Issue with sklearn update 0.22 - Attribute Error

  • #2002: BUG: Fix workflows IO FetchFlow all dataset fetching

  • #1995: ModuleNotFoundError: No module named ‘numpy.testing.decorators’ (Numpy 1.18)

  • #2000: NF: SplitFlow

  • #1999: add cenir_multib to dipy_fetch workflows

  • #1998: [DOC] Workflows Tutorial

  • #1993: [ENH][BF] Error handling for IVIM VarPro NLLS

  • #1870: Documentation example of MSMT CSD

  • #1988: DOC: Multi-Shell Multi-Tissue CSD Example

  • #1975: Azure CI

  • #1953: Deprecate Reconst*Flow

  • #1994: MAINT: Update gradient for SciPy deprecation

  • #1992: MD bad / FA good

  • #1711: ENH: Improve the point distribution algorithm over the sphere.

  • #184: RF/OPT: Use scipy.optimize instead of dipy.core.sphere.disperse_charges

  • #1989: DOC: Fix parameter docstring in dipy.io.streamline.load_tractogram

  • #1982: small bug in recobundles for mam

  • #1987: BF: use MAM distance when that is requested.

  • #1986: Fix the random state for SLR and Recobundles in bundle_extraction.

  • #1976: Better warning when dipy is installed without fury

  • #1977: Add a warning on attempted import.

  • #785: WIP: TST: Add OSX to Travis.

  • #1859: Update Travis design

  • #1950: StatefullTractogram error in Horizon

  • #1983: [Fix] one example

  • #1930: dipy.io.peaks.load_peaks() IOError: This function supports only PAM5 (HDF5) files

  • #1981: DOC: Improve the doc/examples/README file contents

  • #1980: DOC: Improve the doc/README file contents

  • #1978: DOC: Add extension to doc/examples/README file

  • #1979: DOC: Change the doc/README file extension to lowercase

  • #1968: Broken site links (404) on new website when accessed from google

  • #1972: Small fix in warning message

  • #1960: DOC: MCSD Tutorial

  • #1867: WIP: CircleCI

  • #1956: stateful_tractogram_post_1.0_fixes

  • #1971: fix broken link of devel

  • #1970: DOC: Fix typos

  • #1929: ENH: Relocate the sim_response method to allow reuse

  • #1966: ENH: Speed up Cython, remove warnings

  • #1967: ENH: Use language level 3

  • #1954: WIP: Second series of updates and fixes for Horizon

  • #1964: Added a line break

  • #1962: DOC: Display master branch AppVeyor status

  • #1961: STYLE: Remove unused import statements

  • #1963: DOC: Fix parameter docstring in LiFE tracking script

  • #1900: ENH: Add streamline deformation example and workflow

  • #1840: Tutorial showing how to apply deformations to streamlines

  • #1948: Minor Fix for Cross-Validation Example

  • #1951: [FIX] update some utilities scripts

  • #1841: Lab meetings, summer 2019

  • #1958: Adding Missing References in SHORE docs

  • #1955: where is intersphinx inventory under new website domain?

  • #1401: Workflows documentation needs more work

  • #1442: ENH: Minor presentation enhancement to AffineMap object

  • #1791: ENH: Save seeds in TRK/TCK