diff --git a/.circleci/config.yml b/.circleci/config.yml index a90f6f955..d260498de 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -5,7 +5,7 @@ orbs: .dockersetup: &dockersetup docker: - - image: pennlinc/xcp_d_build:0.0.6rc15 + - image: pennlinc/xcp_d_build:0.0.7 working_directory: /src/xcp_d runinstall: diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 075d7f23c..fb5501f19 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -32,6 +32,6 @@ jobs: run: python -m pip install \ flake8 flake8-absolute-import flake8-black flake8-docstrings \ flake8-isort flake8-pyproject flake8-unused-arguments \ - flake8-use-fstring flake8-warnings pep8-naming + flake8-use-fstring pep8-naming - name: Check xcp_d run: python -m flake8 xcp_d diff --git a/CITATION.cff b/CITATION.cff index 470e03735..a52bb4d13 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -86,5 +86,5 @@ keywords: - BIDS-App - Neuroimaging license: BSD-3-Clause -version: 0.4.0 -date-released: '2023-06-12' +version: 0.5.0 +date-released: '2023-09-13' diff --git a/Dockerfile b/Dockerfile index 66fc65876..b8d503252 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM pennlinc/xcp_d_build:0.0.6rc15 +FROM pennlinc/xcp_d_build:0.0.7 # Install xcp_d COPY . /src/xcp_d diff --git a/docs/changes.md b/docs/changes.md index 6636ebd84..c78706020 100644 --- a/docs/changes.md +++ b/docs/changes.md @@ -1,5 +1,45 @@ # What's New +## 0.5.0 + +The 0.5.0 release prepares for the XCP-D manuscript, so I plan to not introduce any backwards-incompatible changes between this release and 1.0.0 (the official paper release). + + +### 🛠 Breaking Changes +* Add CIFTI subcortical atlas to XCP-D by @tsalo in https://github.com/PennLINC/xcp_d/pull/864 +* Change "ciftiSubcortical" atlas name to "HCP" by @tsalo in https://github.com/PennLINC/xcp_d/pull/932 +### 🎉 Exciting New Features +* Write out top-level sidecar for PennLINC QC file by @tsalo in https://github.com/PennLINC/xcp_d/pull/894 +* Parcellate ReHo, ALFF, and surface morphometric maps by @tsalo in https://github.com/PennLINC/xcp_d/pull/839 +* Refactor dcan/hcp ingestion and add more surface files by @tsalo in https://github.com/PennLINC/xcp_d/pull/887 +* Add "none" option for denoising by @tsalo in https://github.com/PennLINC/xcp_d/pull/879 +* Add `--exact-time` parameter by @tsalo in https://github.com/PennLINC/xcp_d/pull/885 +* Allow white matter surface suffix to be either "_smoothwm" or "_white" by @tsalo in https://github.com/PennLINC/xcp_d/pull/899 +* Add `--fs-license-file` parameter to command line interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/930 +* Generate executive summary figures without `--dcan-qc` by @tsalo in https://github.com/PennLINC/xcp_d/pull/936 +### 🐛 Bug Fixes +* Standardize executive summary carpet if params is "none" by @tsalo in https://github.com/PennLINC/xcp_d/pull/916 +* Support CIFTI morphometry files and add PNC test data by @tsalo in https://github.com/PennLINC/xcp_d/pull/922 +* Correct ABCD/HCP surface ingression by @tsalo in https://github.com/PennLINC/xcp_d/pull/927 +### Other Changes +* Add contributing documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/893 +* Update changelog and CFF file for 0.4.0 by @tsalo in https://github.com/PennLINC/xcp_d/pull/896 +* Change packaging to use hatch-vcs and pyproject.toml by @tsalo in https://github.com/PennLINC/xcp_d/pull/897 +* Fix description of signal denoising method in docs by @tsalo in https://github.com/PennLINC/xcp_d/pull/898 +* Improve QC sidecar contents by @tsalo in https://github.com/PennLINC/xcp_d/pull/900 +* Rename the parcellated ALFF/ReHo outputs by @tsalo in https://github.com/PennLINC/xcp_d/pull/902 +* Remove workaround for nonbinary Nibabies brain masks by @tsalo in https://github.com/PennLINC/xcp_d/pull/905 +* Update Landing Page Figure by @kahinimehta in https://github.com/PennLINC/xcp_d/pull/908 +* Remove unused functions in filemanip module by @tsalo in https://github.com/PennLINC/xcp_d/pull/911 +* Add tests for xcp_d.utils.utils module by @tsalo in https://github.com/PennLINC/xcp_d/pull/910 +* Add tests for xcp_d.utils.execsummary module by @tsalo in https://github.com/PennLINC/xcp_d/pull/912 +* Expand tests by @tsalo in https://github.com/PennLINC/xcp_d/pull/913 +* Test CLI parameter validation by @tsalo in https://github.com/PennLINC/xcp_d/pull/918 +* Refactor collection functions by @tsalo in https://github.com/PennLINC/xcp_d/pull/917 + + +**Full Changelog**: https://github.com/PennLINC/xcp_d/compare/04.0...0.5.0 + ## 0.4.0 ### 🛠 Breaking Changes diff --git a/docs/links.rst b/docs/links.rst index 2193dcdbc..6f5222391 100644 --- a/docs/links.rst +++ b/docs/links.rst @@ -10,3 +10,5 @@ .. _`Docker installation`: https://docs.docker.com/install/ .. _`Docker Hub`: https://hub.docker.com/r/pennlinc/xcp_d/tags .. _`Singularity`: https://sylabs.io/guides/3.5/user-guide/introduction.html +.. _`QSIPrep`: https://qsiprep.readthedocs.io +.. _`ASLPrep`: https://aslprep.readthedocs.io diff --git a/docs/outputs.rst b/docs/outputs.rst index ccf1b29be..fa6b0bb69 100644 --- a/docs/outputs.rst +++ b/docs/outputs.rst @@ -5,16 +5,16 @@ Outputs of *XCP-D* ################## -The ``xcp_d`` outputs are written out in BIDS format and consist of three main parts. +The *XCP-D* outputs are written out in BIDS format and consist of three main parts. .. admonition:: A note on BIDS compliance - ``xcp_d`` attempts to follow the BIDS specification as best as possible. - However, many ``xcp_d`` derivatives are not currently covered by the specification. + *XCP-D* attempts to follow the BIDS specification as best as possible. + However, many *XCP-D* derivatives are not currently covered by the specification. In those instances, we attempt to follow recommendations from existing BIDS Extension Proposals (BEPs), which are in-progress proposals to add new features to BIDS. - Three BEPs that are of particular use in ``xcp_d`` are + Three BEPs that are of particular use in *XCP-D* are `BEP012: Functional preprocessing derivatives `_, `BEP017: BIDS connectivity matrix data schema `_, and @@ -24,8 +24,8 @@ The ``xcp_d`` outputs are written out in BIDS format and consist of three main In cases where a derivative type is not covered by an existing BEP, we have simply attempted to follow the general principles of BIDS. - If you discover a problem with the BIDS compliance of ``xcp_d``'s derivatives, please open an - issue in the ``xcp_d`` repository. + If you discover a problem with the BIDS compliance of *XCP-D*'s derivatives, please open an + issue in the *XCP-D* repository. *************** @@ -44,6 +44,33 @@ The executive summary is based on the DCAN lab's sub-