# 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