prepare release

cpp-lln-lab · Sep 5, 2024 · d8518c3 · d8518c3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,55 +24,55 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-* [ENH] add QA workflow `bidsQA` to find outliers in MRIQC output or to view number of outlier timepoints (for a given metric and threshold) in each functional run #1297 by @Remi-Gau
-* [ENH] add support for one-way ANOVA across groups at the group level #1296 by @Remi-Gau
-* [ENH] allow for 2 sample T-Test, within group T-Test and one-way ANOVA to ne more flexible with respect to what praticipants.tsv column to use to allocate subjects in each group #1296 by @Remi-Gau
-* [ENH] make `addConfoundsToDesignMatrix` a method of `BidsModel` #1294 by @Remi-Gau
-* [ENH] add Apptainer definition #1254 by @Remi-Gau and @monique2208
-* [ENH] allow to copy anat only on raw datasets #1181 by @Remi-Gau
-* [ENH] add option to concatenate runs at subject level to facilite running PPI analysis #1133 by @Remi-Gau
-* [ENH] allow to run substeps of substeps of the bayesian model selection #1145 by @Remi-Gau
-* [ENH] add quality control for GLM using the MACS toolbox to give a goodness of fit and several other information criteria (AIC, BIC) (MATLAB only) #1135  by @Remi-Gau
-* [ENH] add several confound strategies to add to bids stats model and a function to create family of models #1126 by @Remi-Gau
-* [ENH] add CLI to run bayesian model selection #1121 by @Remi-Gau
+* [ENH] add QA workflow `bidsQA` to find outliers in MRIQC output or to view number of outlier timepoints (for a given metric and threshold) in each functional run [1297](https://github.com/cpp-lln-lab/bidspm/pull/1297) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add support for one-way ANOVA across groups at the group level [1296](https://github.com/cpp-lln-lab/bidspm/pull/1296) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] allow for 2 sample T-Test, within group T-Test and one-way ANOVA to ne more flexible with respect to what praticipants.tsv column to use to allocate subjects in each group [1296](https://github.com/cpp-lln-lab/bidspm/pull/1296) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] make `addConfoundsToDesignMatrix` a method of `BidsModel` [1294](https://github.com/cpp-lln-lab/bidspm/pull/1294) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add Apptainer definition [1254](https://github.com/cpp-lln-lab/bidspm/pull/1254) by by [Remi-Gau](https://github.com/Remi-Gau)  and by [monique2208](https://github.com/monique2208)
+* [ENH] allow to copy anat only on raw datasets [1181](https://github.com/cpp-lln-lab/bidspm/pull/1181) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add option to concatenate runs at subject level to facilite running PPI analysis [1133](https://github.com/cpp-lln-lab/bidspm/pull/1133) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] allow to run substeps of substeps of the bayesian model selection [1145](https://github.com/cpp-lln-lab/bidspm/pull/1145) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add quality control for GLM using the MACS toolbox to give a goodness of fit and several other information criteria (AIC, BIC) (MATLAB only) [1135](https://github.com/cpp-lln-lab/bidspm/pull/1135)  by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add several confound strategies to add to bids stats model and a function to create family of models [1126](https://github.com/cpp-lln-lab/bidspm/pull/1126) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add CLI to run bayesian model selection [1121](https://github.com/cpp-lln-lab/bidspm/pull/1121) by by [Remi-Gau](https://github.com/Remi-Gau)
 * [ENH] support label of activations with all atlases [1100](https://github.com/cpp-lln-lab/bidspm/pull/1100) by [Remi-Gau](https://github.com/Remi-Gau)
-* [ENH] add support for session level models #1116 be @Remi-Gau
+* [ENH] add support for session level models [1116](https://github.com/cpp-lln-lab/bidspm/pull/1116) be by [Remi-Gau](https://github.com/Remi-Gau)
 
   - allow to pass dummy contrasts to session level
   - allow inter session contrasts to be computed at the subject level
   - improve naming of contrast to mention bids ses and run
 
-* [ENH] add Bayesian model selection to the python CLI #1292 @Remi-Gau
+* [ENH] add Bayesian model selection to the python CLI [1292](https://github.com/cpp-lln-lab/bidspm/pull/1292) by [Remi-Gau](https://github.com/Remi-Gau)
 
 ### Changed
 
-* [ENH] align specification of F contrasts on the BIDS stats model: they should now be specified as a 2D matrix and not a 1D vector. #1276 @Remi-Gau
-* [DOC] change theme and structure of the documentation #1256 @Remi-Gau
-* [REF] Refactor and update CLI in #1096 @Remi-Gau
-* [ENH] {func}`getData` only loads anat data when requested #1257 @Remi-Gau
-* [ENH] the python CLI now uses sub-commands instead of the named parameter `--action` #1292 @Remi-Gau
+* [ENH] align specification of F contrasts on the BIDS stats model: they should now be specified as a 2D matrix and not a 1D vector. [1276](https://github.com/cpp-lln-lab/bidspm/pull/1276) by [Remi-Gau](https://github.com/Remi-Gau)
+* [DOC] change theme and structure of the documentation [1256](https://github.com/cpp-lln-lab/bidspm/pull/1256) by [Remi-Gau](https://github.com/Remi-Gau)
+* [REF] Refactor and update CLI in [1096](https://github.com/cpp-lln-lab/bidspm/pull/1096) by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] {func}`getData` only loads anat data when requested [1257](https://github.com/cpp-lln-lab/bidspm/pull/1257) by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] the python CLI now uses sub-commands instead of the named parameter `--action` [1292](https://github.com/cpp-lln-lab/bidspm/pull/1292) by [Remi-Gau](https://github.com/Remi-Gau)
 
 ### Deprecated
 
 ### Removed
 
-* [REF] Remove old CLI in #1096 @Remi-Gau
+* [REF] Remove old CLI in [1096](https://github.com/cpp-lln-lab/bidspm/pull/1096) by [Remi-Gau](https://github.com/Remi-Gau)
 
 ### Fixed
 
-* [FIX] ensure that {func}`setBatchCoregistrationFuncToAnat` takes into account bids_filter #1295 by @d-ni374
-* [FIX] update {func}`createDefaultStatsModel` to use proper `GroupBy` at the dataset level #1248 by @d-ni374
-* [FIX] make {func}`getAcquisitionTime` less brittle #1248 by @d-ni374
-* [FIX] fix regular expression in {func}`bidsResults` to identify contrasts #1248 by @d-ni374 and #1275 by @Remi-Gau
-* [FIX] pass analysis level to stats actions when using python CLI #1258 @Remi-Gau
-* [FIX] remove goodness of fit from dataset level analysis as it is not supported by the MACS toolbox #1265 by @Remi-Gau
-* [FIX] add java and zip to container recipes to allow using nidm results with octave #1265 by @Remi-Gau
-* [FIX] copy the MACS toolbox to the SPM toolbox folder during the initialisation #1203 by @Remi-Gau
-* [FIX] save `onsets.mat` directly in subject stats folder #1187 by @Remi-Gau
-* [FIX] do not compute subject level contrast when running dataset level #1102 by @Remi-Gau
-* [FIX] copy `RepetitionTime` in sidecar JSON after running smoothing in #1099 by @Remi-Gau
-* [FIX] rename results files (csv, tsv, png, nii) of each contrasts #1104 by @Remi-Gau
-* [FIX] reslice ROIS before running ROI based analysis to make sure they are at the resolution of the BOLD images in #1110 by @Remi-Gau
+* [FIX] ensure that {func}`setBatchCoregistrationFuncToAnat` takes into account bids_filter [1295](https://github.com/cpp-lln-lab/bidspm/pull/1295) by by [d-ni374](https://github.com/d-ni374)
+* [FIX] update {func}`createDefaultStatsModel` to use proper `GroupBy` at the dataset level [1248](https://github.com/cpp-lln-lab/bidspm/pull/1248) by by [d-ni374](https://github.com/d-ni374)
+* [FIX] make {func}`getAcquisitionTime` less brittle [1248](https://github.com/cpp-lln-lab/bidspm/pull/1248) by by [d-ni374](https://github.com/d-ni374)
+* [FIX] fix regular expression in {func}`bidsResults` to identify contrasts [1248](https://github.com/cpp-lln-lab/bidspm/pull/1248) by by [d-ni374](https://github.com/d-ni374)  and [1275](https://github.com/cpp-lln-lab/bidspm/pull/1275) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] pass analysis level to stats actions when using python CLI [1258](https://github.com/cpp-lln-lab/bidspm/pull/1258) by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] remove goodness of fit from dataset level analysis as it is not supported by the MACS toolbox [1265](https://github.com/cpp-lln-lab/bidspm/pull/1265) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] add java and zip to container recipes to allow using nidm results with octave [1265](https://github.com/cpp-lln-lab/bidspm/pull/1265) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] copy the MACS toolbox to the SPM toolbox folder during the initialisation [1203](https://github.com/cpp-lln-lab/bidspm/pull/1203) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] save `onsets.mat` directly in subject stats folder [1187](https://github.com/cpp-lln-lab/bidspm/pull/1187) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] do not compute subject level contrast when running dataset level [1102](https://github.com/cpp-lln-lab/bidspm/pull/1102) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] copy `RepetitionTime` in sidecar JSON after running smoothing in [1099](https://github.com/cpp-lln-lab/bidspm/pull/1099) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] rename results files (csv, tsv, png, nii) of each contrasts [1104](https://github.com/cpp-lln-lab/bidspm/pull/1104) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] reslice ROIS before running ROI based analysis to make sure they are at the resolution of the BOLD images in [1110](https://github.com/cpp-lln-lab/bidspm/pull/1110) by by [Remi-Gau](https://github.com/Remi-Gau)
 
 ### Security
 
@@ -252,7 +252,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * [FIX] various bug fixes in [694](https://github.com/cpp-lln-lab/bidspm/pull/694) by [Remi-Gau](https://github.com/Remi-Gau)
 * [FIX] add some warnings to handle several bugs with empty ROIs in [693](https://github.com/cpp-lln-lab/bidspm/pull/693) by [Remi-Gau](https://github.com/Remi-Gau)
 * [FIX] re enable octave tests CI in [686](https://github.com/cpp-lln-lab/bidspm/pull/686) by [Remi-Gau](https://github.com/Remi-Gau)
-* [FIX] patches for [682](https://github.com/cpp-lln-lab/bidspm/pull/682) and  [683](https://github.com/cpp-lln-lab/bidspm/pull/683) (#687) by [mwmaclean](https://github.com/mwmaclean)
+* [FIX] patches for [682](https://github.com/cpp-lln-lab/bidspm/pull/682) and  [683](https://github.com/cpp-lln-lab/bidspm/pull/683) ([687](https://github.com/cpp-lln-lab/bidspm/pull/687)) by [mwmaclean](https://github.com/mwmaclean)
 * [FIX] ensure that bidsResults does not run if we don't have the proper options in [679](https://github.com/cpp-lln-lab/bidspm/pull/679) by [Remi-Gau](https://github.com/Remi-Gau)
 * [FIX] returnRootDir only relies on fullpaths in [676](https://github.com/cpp-lln-lab/bidspm/pull/676) by [Remi-Gau](https://github.com/Remi-Gau)
 * [FIX] set minimum compatible fmriprep version in [675](https://github.com/cpp-lln-lab/bidspm/pull/675) by [Remi-Gau](https://github.com/Remi-Gau)

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,120 +1,121 @@
 cff-version: 1.2.0
 
-title: "bidspm"
+title: bidspm
 
-version: 3.1.0dev
+version: 4.0.0
 
-abstract: bidspm is a set of pipelines and tools for Octave / MATLAB to process and analyze BIDS data sets using SPM12.
+abstract: bidspm is a set of pipelines and tools for Octave / MATLAB to process and
+  analyze BIDS data sets using SPM12.
 
-message: "If you use this software, please cite it as below."
+message: If you use this software, please cite it as below.
 
-repository-code: "https://github.com/cpp-lln-lab/bidspm"
+repository-code: https://github.com/cpp-lln-lab/bidspm
 
 identifiers:
   - description: This is the collection of archived snapshots of all releases of bidspm
     type: doi
-    value: "10.5281/zenodo.3554331"
+    value: 10.5281/zenodo.3554331
   - description: OHBM 2023 poster
     type: doi
-    value: "10.5281/zenodo.8099835"
+    value: 10.5281/zenodo.8099835
 
 contact:
-  - affiliation: "Université catholique de Louvain"
+  - affiliation: Université catholique de Louvain
     email: remi.gau2@mcgill.ca
     family-names: Gau
     given-names: Rémi
 
 authors:
-- family-names: "Gau"
-  given-names: "Rémi"
-  orcid: "https://orcid.org/0000-0002-1535-9767"
-  affiliation: "Origami lab, McGill University, Montreal, Québec, Canada"
-
-- family-names: "Barilari"
-  given-names: "Marco"
-  orcid: "https://orcid.org/0000-0002-3313-3120"
-  affiliation: "Université catholique de Louvain"
-
-- family-names: "Battal"
-  given-names: "Ceren"
-  orcid: "https://orcid.org/0000-0002-9844-7630"
-  affiliation: "Université catholique de Louvain"
-
-- family-names: "Rezk"
-  given-names: "Mohamed"
-  orcid: "https://orcid.org/0000-0002-1866-8645"
-  affiliation: "Université catholique de Louvain"
-
-- family-names: "Gurtubay"
-  given-names: "Ane"
-  orcid: "https://orcid.org/0000-0003-3824-2219"
-  affiliation: "Université catholique de Louvain"
-
-- family-names: "Falagiarda"
-  given-names: "Federica"
-  orcid: "https://orcid.org/0000-0001-7844-1605"
-  affiliation: "Université catholique de Louvain"
-
-- family-names: "MacLean"
-  given-names: "Michèle"
-  orcid: "https://orcid.org/0000-0002-0174-9326"
-  affiliation: "Université de Montréal"
-
-- family-names: "Cerpelloni"
-  given-names: "Filippo"
-  orcid: "https://orcid.org/0000-0001-8070-5753"
-  affiliation: "Université catholique de Louvain"
-
-- family-names: "Shahzad"
-  given-names: "Iqra"
-  orcid: "https://orcid.org/0000-0002-8724-7668"
-  affiliation: "Université catholique de Louvain"
-
-- family-names: "Nunes"
-  given-names: "Márcia"
-
-- family-names: "Caron-Guyon"
-  given-names: "Jeanne"
-  orcid: "https://orcid.org/0000-0001-8681-5267"
-  affiliation: "Université catholique de Louvain"
-
-- family-names: "Chouinard-Leclaire"
-  given-names: "Christine"
-  orcid: "https://orcid.org/0000-0002-1066-6266"
-  affiliation: "Université de Montréal"
-
-- family-names: "Yang"
-  given-names: "Ying"
-  orcid: "https://orcid.org/0000-0002-4157-2975"
-  affiliation: "Université catholique de Louvain"
-
-- family-names: "Mattioni"
-  given-names: "Stefania"
-  affiliation: "University of Gent"
-  orcid: "https://orcid.org/0000-0001-8279-6118"
-
-- family-names: Huber
-  given-names:  Daniel
-  affiliation: University of Innsbruck
-
-- family-names: "Van Audenhaege"
-  given-names:  "Alice"
-  affiliation: "Université catholique de Louvain"
-  orcid: "https://orcid.org/0000-0002-5276-8818"
-
-- family-names: "Matuszewski"
-  given-names:  "Jacek"
-  affiliation: "Université catholique de Louvain"
-  orcid: "https://orcid.org/0000-0001-9752-3294"
-
-- family-names: "Collignon"
-  given-names: "Olivier"
-  orcid: "https://orcid.org/0000-0003-1882-3550"
-  affiliation: "Université catholique de Louvain"
-
-- family-names: "Denissen"
-  given-names: "Monique"
-
+  - family-names: Van Audenhaege
+    given-names: Alice
+    affiliation: Université catholique de Louvain
+    orcid: https://orcid.org/0000-0002-5276-8818
+
+  - family-names: Gurtubay
+    given-names: Ane
+    orcid: https://orcid.org/0000-0003-3824-2219
+    affiliation: Université catholique de Louvain
+
+  - family-names: Battal
+    given-names: Ceren
+    orcid: https://orcid.org/0000-0002-9844-7630
+    affiliation: Université catholique de Louvain
+
+  - family-names: Chouinard-Leclaire
+    given-names: Christine
+    orcid: https://orcid.org/0000-0002-1066-6266
+    affiliation: Université de Montréal
+
+  - family-names: Huber
+    given-names: Daniel
+    affiliation: University of Innsbruck
+
+  - family-names: Falagiarda
+    given-names: Federica
+    orcid: https://orcid.org/0000-0001-7844-1605
+    affiliation: Université catholique de Louvain
+
+  - family-names: Cerpelloni
+    given-names: Filippo
+    orcid: https://orcid.org/0000-0001-8070-5753
+    affiliation: Université catholique de Louvain
+
+  - family-names: Shahzad
+    given-names: Iqra
+    orcid: https://orcid.org/0000-0002-8724-7668
+    affiliation: Université catholique de Louvain
+
+  - family-names: Matuszewski
+    given-names: Jacek
+    affiliation: Université catholique de Louvain
+    orcid: https://orcid.org/0000-0001-9752-3294
+
+  - family-names: Caron-Guyon
+    given-names: Jeanne
+    orcid: https://orcid.org/0000-0001-8681-5267
+    affiliation: Université catholique de Louvain
+
+  - family-names: Barilari
+    given-names: Marco
+    orcid: https://orcid.org/0000-0002-3313-3120
+    affiliation: Université catholique de Louvain
+
+  - family-names: MacLean
+    given-names: Michèle
+    orcid: https://orcid.org/0000-0002-0174-9326
+    affiliation: Université de Montréal
+
+  - family-names: Rezk
+    given-names: Mohamed
+    orcid: https://orcid.org/0000-0002-1866-8645
+    affiliation: Université catholique de Louvain
+
+  - family-names: Denissen
+    given-names: Monique
+
+
+  - family-names: Nunes
+    given-names: Márcia
+
+  - family-names: Collignon
+    given-names: Olivier
+    orcid: https://orcid.org/0000-0003-1882-3550
+    affiliation: Université catholique de Louvain
+
+  - family-names: Gau
+    given-names: Rémi
+    orcid: https://orcid.org/0000-0002-1535-9767
+    affiliation: Origami lab, McGill University, Montreal, Québec, Canada
+
+  - family-names: Mattioni
+    given-names: Stefania
+    affiliation: University of Gent
+    orcid: https://orcid.org/0000-0001-8279-6118
+
+  - family-names: Yang
+    given-names: Ying
+    orcid: https://orcid.org/0000-0002-4157-2975
+    affiliation: Université catholique de Louvain
 
 license: GPL-3.0
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -116,3 +116,5 @@ make update_faq
 - [ ] merge to default branch
 - [ ] create a tagged release
 - [ ] build and push docker images if necessary
+- [ ] after release
+  - [ ] set version in `citation.cff` to dev
diff --git a/Makefile b/Makefile
@@ -61,37 +61,14 @@ fix_submodule: ## Fix any submodules that would not be checked out
 
 prepare_release:
 	python tools/citation_cff_maint.py
-	python tools/tools/add_links_to_changelog.py
+	python tools/add_links_to_changelog.py
 	python tools/bump_version.py
+	cd docs && make release
 
 validate_cff: ## Validate the citation file
 	cffconvert --validate
 
-release: validate_cff prepare_release lint manual
-
-
-################################################################################
-#   doc
-
-clean_doc:
-	cd docs && make clean
-
-manual: update_faq ## Build PDF version of the doc
-	cd docs && sh create_manual.sh
-
-
-################################################################################
-#   lint
-
-lint: lint_matlab lint_python ## Clean MATLAB and python code
-
-lint_matlab: ## Clean MATLAB code
-	mh_style --fix && mh_metric --ci && mh_lint
-
-lint_python: ## Clean python code
-	black *.py src tests docs
-	flake8	*.py src tests docs
-	mypy *.py src
+release: validate_cff prepare_release
 
 ################################################################################
 #   test

diff --git a/README.md b/README.md
@@ -169,7 +169,7 @@ Please see our [documentation](https://bidspm.readthedocs.io/en/latest/index.htm
   license = {GPL-3.0},
   title = {{bidspm}},
   url = {https://github.com/cpp-lln-lab/bidspm},
-  version = {3.1.0dev}
+  version = {4.0.0}
 }
 ```
 

diff --git a/docs/Makefile b/docs/Makefile
@@ -33,11 +33,13 @@ help:
 
 clean:
 	rm -rf $(BUILDDIR)
-	rm -f bidspm-manual.pdf
 
 view:
 	$(BROWSER) build/html/index.html
 
+release: update_faq boilerplate clean_default_options default_mapping
+	python generate_doc.py
+
 update_faq:
 	cd faq/bids && faqtory build
 	cd faq/general && faqtory build
@@ -46,9 +48,6 @@ update_faq:
 	cd faq/spm && faqtory build
 	cd faq/stats && faqtory build
 
-bidspm-manual.pdf: update_faq
-	bash create_manual.sh
-
 boilerplate:
 	$(MATLAB) $(ARG) -r "print_boilerplate; exit()"
 	rm -fr reports