Version 1 release 🥳

.flake8

@@ -0,0 +1,4 @@
+[flake8]
+ignore = E203, E231, W503, E722
+max-line-length = 79
+exclude = __init__.py,build,.eggs

.github/workflows/test_and_deploy.yml

@@ -42,9 +42,15 @@ jobs:
         with:
             path: ~/.brainglobe
             key: atlases
-      - uses: neuroinformatics-unit/actions/test@v2
+
+      - name: Setup QT libraries
+        uses: tlambert03/setup-qt-libs@v1
+
+      - name: Run tests
+        uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          use-xvfb: true
 
   test-with-conda:
     needs: [linting, manifest]

.gitignore

@@ -2,7 +2,7 @@
 *.conf.custom
 
 # Byte-compiled / optimized / DLL files
-__pycache__/
+**/__pycache__/
 *.py[cod]
 *$py.class
 
@@ -122,3 +122,4 @@ tests/data/test_output
 
 
 *.DS_Store
+pip-wheel-metadata/

.napari/config.yml

@@ -0,0 +1,7 @@
+labels:
+  ontology: EDAM-BIOIMAGING:alpha06
+  terms:
+  - Image registration
+  - Affine registration
+  - Multi-channel
+summary: Multi-atlas whole-brain microscopy registration

CITATION.cff

@@ -0,0 +1,102 @@
+
+cff-version: 1.2.0
+message: If you use this software, please cite it using these metadata.
+title: brainreg
+authors:
+- family-names: "Tyson"
+  given-names: "A."
+- family-names: "Vélez-Fort"
+  given-names: "M."
+- family-names: "Rousseau"
+  given-names: "C."
+- family-names: "Cossell"
+  given-names: "L."
+- family-names: "Tsitoura"
+  given-names: " C."
+- family-names: "Lenzi"
+  given-names: " S."
+- family-names: "Obenhaus"
+  given-names: "H."
+- family-names: "Claudi"
+  given-names: "F."
+- family-names: "Branco"
+  given-names: "T."
+- family-names: "Margrie"
+  given-names: "T."
+url: https://github.com/brainglobe/brainreg
+preferred-citation:
+    type: article
+    title: Accurate determination of marker location within whole-brain microscopy images
+    journal: Scientific Reports
+    volume: 12
+    pages: 867
+    doi: 10.1038/s41598-021-04676-9
+    year: 2022
+    date-published: 2022-01-18
+    authors:
+      - family-names: "Tyson"
+        given-names: "A."
+      - family-names: "Vélez-Fort"
+        given-names: "M."
+      - family-names: "Rousseau"
+        given-names: "C."
+      - family-names: "Cossell"
+        given-names: "L."
+      - family-names: "Tsitoura"
+        given-names: " C."
+      - family-names: "Lenzi"
+        given-names: "S."
+      - family-names: "Obenhaus"
+        given-names: "H."
+      - family-names: "Claudi"
+        given-names: "F."
+      - family-names: "Branco"
+        given-names: "T."
+      - family-names: "Margrie"
+        given-names: "T."
+references:
+  - type: article
+    title: AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data
+    journal: Nature Communications
+    volume: 7
+    pages: 1-9
+    doi: 10.1038/ncomms11879
+    year: 2016
+    date-published: 2016-07-07
+    authors:
+      - family-names: "Niedworok"
+        given-names: "C."
+      - family-names: "Brown"
+        given-names: "A."
+      - family-names: "Jorge"
+        given-names: "M."
+      - family-names: "Osten"
+        given-names: "P."
+      - family-names: "Ourselin"
+        given-names: "S."
+      - family-names: "Modat"
+        given-names: "M."
+      - family-names: "Margrie"
+        given-names: "T."
+references:
+  - type: article
+    title: BrainGlobe Atlas API a common interface for neuroanatomical atlases
+    journal: Journal of Open Source Software
+    volume: 5
+    pages: 2668
+    doi: 10.21105/joss.02668
+    year: 2020
+    date-published: 2020-09-04
+    authors:
+      - family-names: "Claudi"
+        given-names: "F."
+      - family-names: "Petrucco"
+        given-names: "L."
+      - family-names: "Tyson"
+        given-names: "A."
+      - family-names: "Branco"
+        given-names: "T."
+      - family-names: "Margrie"
+        given-names: "T."
+      - family-names: "Portugues"
+        given-names: "R."

MANIFEST.in

@@ -1,17 +1,22 @@
 include LICENSE
 include README.md
+include CITATION.cff
 
-prune tests
+exclude .flake8
+exclude .pre-commit-config.yaml
+exclude *.yml
 exclude tox.ini
 
-exclude *.yaml
-exclude *.yml
+include brainreg/napari/napari.yaml
 
-recursive-include src *.dll
-recursive-include src *.exe
-recursive-include src *.txt
+recursive-include brainreg/core *.dll
+recursive-include brainreg/core *.exe
+recursive-include brainreg/core *.txt
+recursive-include brainreg/core/bin/nifty_reg/linux_x64 *
+recursive-include brainreg/core/bin/nifty_reg/osX *
 
-recursive-exclude src *.zip
+recursive-exclude .napari *
+recursive-exclude brainreg/core *.zip
+recursive-exclude examples *
 
-recursive-include src/brainreg/bin/nifty_reg/linux_x64 *
-recursive-include src/brainreg/bin/nifty_reg/osX *
+prune tests