Repository: NIRALUser/NeuroRuler (language: python)

Issue:
Better data management.
![image](https://user-images.githubusercontent.com/54514192/234318468-bb63a735-cc7a-483c-b95a-deb26035e13e.png)
![image](https://user-images.githubusercontent.com/54514192/234318607-20f02d11-2c4e-4937-ba04-c34b18f67f7e.png)
nani?? Why do I have to do all this stuff for my test to work locally? Why isn't this automated? @jesse-wei fix ittt plzzzzz


Discussion / hints:
I think it would better to just have all the data we need in the repo, even if this makes the repo quite big. (as Jesse just mentioned, users using `pip` wouldn't be affected by this, just the developers)
> I think it would better to just have all the data we need in the repo, even if this makes the repo quite big. (as Jesse just mentioned, users using `pip` wouldn't be affected by this, just the developers)

Yeah, this is fine. Users would use `pip` and wouldn't download the data. Agree that downloading into data/ during CI test and gitignoring has been super convoluted.
I also don't trust dropbox to permanently hold this data (speaking from personal experience)

Fix patch:
diff --git a/.gitignore b/.gitignore
index 95d8005..e2250f7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,22 +1,10 @@
-# You should upload new data into your local data/, but don't commit it to the repo
-# Data will be downloaded into data/ during GitHub CI tests
-# See .github/workflows/tests.yml
-data/*.nrrd
-data/*.nii.gz
-data/*.nii
-data/*.tsv
-
 output/
 scripts/pypi
 scripts/pypi_upload
 scripts/testpypi
 scripts/testpypi_upload
 
-.ipynb_checkpoints
 .DS_Store
-venv/
-.idea/
-.tox/
 Playground/imgproc/contour_numpy.txt
 Playground/imgproc/contour_sitk.txt
 Playground/imgproc/numpy_array_255.png
@@ -24,10 +12,7 @@ NeuroRuler/HeadCircumferenceTool.egg-info
 tests/noise_vals.txt
 tests/noise_vals_copy.txt
 out/
-.pytest_cache/
-__pycache__/
 bin/
-lib/
 etc/
 include/
 share/
diff --git a/data/150649_V06_HeadCirc.tsv b/data/150649_V06_HeadCirc.tsv
new file mode 100644
index 0000000..e46a61e
--- /dev/null
+++ b/data/150649_V06_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/150649/V06/mri/registered_v3.6/sMRI/	stx_noscale_150649_V06_t1w	438.271897
diff --git a/data/150649_V06_t1w.nrrd b/data/150649_V06_t1w.nrrd
new file mode 100644
index 0000000..56d15fd
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diff --git a/data/150649_V24_HeadCirc.tsv b/data/150649_V24_HeadCirc.tsv
new file mode 100644
index 0000000..51e8626
--- /dev/null
+++ b/data/150649_V24_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/150649/V24/mri/registered_v3.6/sMRI/	stx_noscale_150649_V24_t1w	488.917926
diff --git a/data/150649_V24_t1w.nrrd b/data/150649_V24_t1w.nrrd
new file mode 100644
index 0000000..c559d99
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diff --git a/data/150649_V36_HeadCirc.tsv b/data/150649_V36_HeadCirc.tsv
new file mode 100644
index 0000000..0268926
--- /dev/null
+++ b/data/150649_V36_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/150649/V36/mri/registered_v3.6/sMRI/	stx_noscale_150649_V36_t1w	498.056745
diff --git a/data/150649_V36_t1w.nrrd b/data/150649_V36_t1w.nrrd
new file mode 100644
index 0000000..52c7f97
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diff --git a/data/152174_V03_HeadCirc.tsv b/data/152174_V03_HeadCirc.tsv
new file mode 100644
index 0000000..efff7f9
--- /dev/null
+++ b/data/152174_V03_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/152174/V03/mri/registered_v3.10/sMRI/	stx_noscale_152174_V03_t1w	406.261736
diff --git a/data/152174_V03_t1w.nrrd b/data/152174_V03_t1w.nrrd
new file mode 100644
index 0000000..01ffd89
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diff --git a/data/155712_V06_HeadCirc.tsv b/data/155712_V06_HeadCirc.tsv
new file mode 100644
index 0000000..8e7a07d
--- /dev/null
+++ b/data/155712_V06_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/155712/V06/mri/registered_v3.6/sMRI/	stx_noscale_155712_V06_t1w	465.281856
diff --git a/data/155712_V06_t1w.nrrd b/data/155712_V06_t1w.nrrd
new file mode 100644
index 0000000..9cbcb78
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diff --git a/data/155712_V24_HeadCirc.tsv b/data/155712_V24_HeadCirc.tsv
new file mode 100644
index 0000000..ef2a9f5
--- /dev/null
+++ b/data/155712_V24_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/155712/V24/mri/registered_v3.6/sMRI/	stx_noscale_155712_V24_t1w	518.555482
diff --git a/data/155712_V24_t1w.nrrd b/data/155712_V24_t1w.nrrd
new file mode 100644
index 0000000..d3ca3f6
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diff --git a/data/157746_V06_HeadCirc.tsv b/data/157746_V06_HeadCirc.tsv
new file mode 100644
index 0000000..7241484
--- /dev/null
+++ b/data/157746_V06_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/157746/V06/mri/registered_v3.6/sMRI/	stx_noscale_157746_V06_t1w	448.930576
diff --git a/data/157746_V06_t1w.nrrd b/data/157746_V06_t1w.nrrd
new file mode 100644
index 0000000..047ebc3
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diff --git a/data/157746_V12_HeadCirc.tsv b/data/157746_V12_HeadCirc.tsv
new file mode 100644
index 0000000..302f64b
--- /dev/null
+++ b/data/157746_V12_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/157746/V12/mri/registered_v3.6/sMRI/	stx_noscale_157746_V12_t1w	482.759229
diff --git a/data/157746_V12_t1w.nrrd b/data/157746_V12_t1w.nrrd
new file mode 100644
index 0000000..8b592eb
Binary files /dev/null and b/data/157746_V12_t1w.nrrd differ
diff --git a/data/158296_V03_HeadCirc.tsv b/data/158296_V03_HeadCirc.tsv
new file mode 100644
index 0000000..6886ac8
--- /dev/null
+++ b/data/158296_V03_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/158296/V03/mri/registered_v3.6/sMRI/	stx_noscale_158296_V03_t1w	424.044551
diff --git a/data/158296_V03_t1w.nrrd b/data/158296_V03_t1w.nrrd
new file mode 100644
index 0000000..d97c90f
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diff --git a/data/158296_V24_HeadCirc.tsv b/data/158296_V24_HeadCirc.tsv
new file mode 100644
index 0000000..a9d2ec8
--- /dev/null
+++ b/data/158296_V24_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/158296/V24/mri/registered_v3.10/sMRI/	stx_noscale_158296_V24_t1w	513.178328
diff --git a/data/158296_V24_t1w.nrrd b/data/158296_V24_t1w.nrrd
new file mode 100644
index 0000000..0f82d10
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diff --git a/data/341870_V06_HeadCirc.tsv b/data/341870_V06_HeadCirc.tsv
new file mode 100644
index 0000000..022ce0e
--- /dev/null
+++ b/data/341870_V06_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/341870/V06/mri/registered_v3.6/sMRI/	stx_noscale_341870_V06_t1w	457.788365
diff --git a/data/341870_V06_t1w.nrrd b/data/341870_V06_t1w.nrrd
new file mode 100644
index 0000000..e7f1590
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diff --git a/data/341870_V12_HeadCirc.tsv b/data/341870_V12_HeadCirc.tsv
new file mode 100644
index 0000000..872a8e8
--- /dev/null
+++ b/data/341870_V12_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/341870/V12/mri/registered_v3.6/sMRI/	stx_noscale_341870_V12_t1w	485.324805
diff --git a/data/341870_V12_t1w.nrrd b/data/341870_V12_t1w.nrrd
new file mode 100644
index 0000000..e9cb59b
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diff --git a/data/341870_V24_HeadCirc.tsv b/data/341870_V24_HeadCirc.tsv
new file mode 100644
index 0000000..442a7a2
--- /dev/null
+++ b/data/341870_V24_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/341870/V24/mri/registered_v3.6/sMRI/	stx_noscale_341870_V24_t1w	503.457440
diff --git a/data/341870_V24_t1w.nrrd b/data/341870_V24_t1w.nrrd
new file mode 100644
index 0000000..368b7d0
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diff --git a/data/341870_V36_HeadCirc.tsv b/data/341870_V36_HeadCirc.tsv
new file mode 100644
index 0000000..4ffdcb0
--- /dev/null
+++ b/data/341870_V36_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/341870/V36/mri/registered_v3.6/sMRI/	stx_noscale_341870_V36_t1w	513.833890
diff --git a/data/341870_V36_t1w.nrrd b/data/341870_V36_t1w.nrrd
new file mode 100644
index 0000000..526abdd
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diff --git a/data/346731_V06_HeadCirc.tsv b/data/346731_V06_HeadCirc.tsv
new file mode 100644
index 0000000..f5d2586
--- /dev/null
+++ b/data/346731_V06_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/346731/V06/mri/registered_v3.6/sMRI/	stx_noscale_346731_V06_t1w	454.390570
diff --git a/data/346731_V06_t1w.nrrd b/data/346731_V06_t1w.nrrd
new file mode 100644
index 0000000..d03295c
Binary files /dev/null and b/data/346731_V06_t1w.nrrd differ
diff --git a/data/346973_V06_HeadCirc.tsv b/data/346973_V06_HeadCirc.tsv
new file mode 100644
index 0000000..d7ccc6e
--- /dev/null
+++ b/data/346973_V06_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/346973/V06/mri/registered_v3.6/sMRI/	stx_noscale_346973_V06_t1w	457.865888
diff --git a/data/346973_V06_t1w.nrrd b/data/346973_V06_t1w.nrrd
new file mode 100644
index 0000000..63f8c77
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diff --git a/data/346973_V12_HeadCirc.tsv b/data/346973_V12_HeadCirc.tsv
new file mode 100644
index 0000000..e3cc0e9
--- /dev/null
+++ b/data/346973_V12_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/346973/V12/mri/registered_v3.6/sMRI/	stx_noscale_346973_V12_t1w	481.864430
diff --git a/data/346973_V12_t1w.nrrd b/data/346973_V12_t1w.nrrd
new file mode 100644
index 0000000..885417b
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diff --git a/data/346973_V24_HeadCirc.tsv b/data/346973_V24_HeadCirc.tsv
new file mode 100644
index 0000000..7c1c3bb
--- /dev/null
+++ b/data/346973_V24_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/346973/V24/mri/registered_v3.6/sMRI/	stx_noscale_346973_V24_t1w	501.664987
diff --git a/data/346973_V24_t1w.nrrd b/data/346973_V24_t1w.nrrd
new file mode 100644
index 0000000..70d395e
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diff --git a/data/347302_V06_HeadCirc.tsv b/data/347302_V06_HeadCirc.tsv
new file mode 100644
index 0000000..82c4edb
--- /dev/null
+++ b/data/347302_V06_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/347302/V06/mri/registered_v3.6/sMRI/	stx_noscale_347302_V06_t1w	437.418598
diff --git a/data/347302_V06_t1w.nrrd b/data/347302_V06_t1w.nrrd
new file mode 100644
index 0000000..1440064
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diff --git a/data/347302_V12_HeadCirc.tsv b/data/347302_V12_HeadCirc.tsv
new file mode 100644
index 0000000..295a218
--- /dev/null
+++ b/data/347302_V12_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/347302/V12/mri/registered_v3.6/sMRI/	stx_noscale_347302_V12_t1w	470.398390
diff --git a/data/347302_V12_t1w.nrrd b/data/347302_V12_t1w.nrrd
new file mode 100644
index 0000000..6fc346b
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diff --git a/data/347302_V24_HeadCirc.tsv b/data/347302_V24_HeadCirc.tsv
new file mode 100644
index 0000000..90fd595
--- /dev/null
+++ b/data/347302_V24_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/347302/V24/mri/registered_v3.6/sMRI/	stx_noscale_347302_V24_t1w	492.281089
diff --git a/data/347302_V24_t1w.nrrd b/data/347302_V24_t1w.nrrd
new file mode 100644
index 0000000..b802546
Binary files /dev/null and b/data/347302_V24_t1w.nrrd differ
diff --git a/data/348547_V24_HeadCirc.tsv b/data/348547_V24_HeadCirc.tsv
new file mode 100644
index 0000000..342bd30
--- /dev/null
+++ b/data/348547_V24_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/348547/V24/mri/registered_v3.6/sMRI/	stx_noscale_348547_V24_t1w	512.053695
diff --git a/data/348547_V24_t1w.nrrd b/data/348547_V24_t1w.nrrd
new file mode 100644
index 0000000..c974126
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diff --git a/data/588132_V09_HeadCirc.tsv b/data/588132_V09_HeadCirc.tsv
new file mode 100644
index 0000000..1ff7005
--- /dev/null
+++ b/data/588132_V09_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/588132/V09/mri/registered_v3.6/sMRI/	stx_noscale_588132_V09_t1w	449.982098
diff --git a/data/588132_V09_t1w.nrrd b/data/588132_V09_t1w.nrrd
new file mode 100644
index 0000000..21d25b5
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diff --git a/data/588132_V12_HeadCirc.tsv b/data/588132_V12_HeadCirc.tsv
new file mode 100644
index 0000000..1c9556a
--- /dev/null
+++ b/data/588132_V12_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/588132/V12/mri/registered_v3.7/sMRI/	stx_noscale_588132_V12_t1w	463.366140
diff --git a/data/588132_V12_t1w.nrrd b/data/588132_V12_t1w.nrrd
new file mode 100644
index 0000000..1191e22
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diff --git a/data/588132_V24_HeadCirc.tsv b/data/588132_V24_HeadCirc.tsv
new file mode 100644
index 0000000..8282613
--- /dev/null
+++ b/data/588132_V24_HeadCirc.tsv
@@ -0,0 +1,1 @@
+/Human/Autism2/IBIS1/IBIS/Proc_Data/588132/V24/mri/registered_v3.10/sMRI/	stx_noscale_588132_V24_t1w	483.996256
diff --git a/data/588132_V24_t1w.nrrd b/data/588132_V24_t1w.nrrd
new file mode 100644
index 0000000..ee9c41d
Binary files /dev/null and b/data/588132_V24_t1w.nrrd differ


Test patch:
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ca77911..9409628 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -5,23 +5,6 @@ on:
   - pull_request
 
 jobs:
-  download-data:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: Install dependencies
-        run: |
-          sudo apt-get install curl
-          sudo apt-get install unzip
-      - name: Download NeuroRuler data into data/
-        # Source: https://stackoverflow.com/questions/21322614/use-curl-to-download-a-dropbox-folder-via-shared-link-not-public-link
-        # Also https://stackoverflow.com/questions/21322416/unzip-warning-and-mapname
-        run: |
-          curl -L -o data.zip https://www.dropbox.com/sh/3k3p0o14rdwrx7p/AAAGSpXdVkyBXAnanPZgwRP4a/?dl/=1
-          unzip data.zip -x / -d data/
-          ls -R data/
-          rm data.zip
-
   test:
     runs-on: ${{ matrix.os }}
     strategy: