From f1197c872a6ece451ae8e1fdd80c162ac59864dc Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 15:01:09 -0400
Subject: [PATCH 01/26] tests

---
 .github/workflows/testing.yml | 32 ++++++++++++++++++++++++++++++++
 tests/test_map_to_map.py      |  5 +++++
 2 files changed, 37 insertions(+)
 create mode 100644 .github/workflows/testing.yml
 create mode 100644 tests/test_map_to_map.py

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
new file mode 100644
index 0000000..4b829dc
--- /dev/null
+++ b/.github/workflows/testing.yml
@@ -0,0 +1,32 @@
+# GHA workflow for running tests. 
+#
+# Largely taken from 
+# https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+# Please check the link for more detailed instructions
+
+name: Run tests
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+          pip install pytest
+      - name: Test with pytest
+        run: |
+          pytest tests/
diff --git a/tests/test_map_to_map.py b/tests/test_map_to_map.py
new file mode 100644
index 0000000..968ab07
--- /dev/null
+++ b/tests/test_map_to_map.py
@@ -0,0 +1,5 @@
+def test_pass():
+    assert True
+
+def test_fail():
+    assert False
\ No newline at end of file

From 991177479ecefe9c1bf6310686db92eff3022df8 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 15:03:46 -0400
Subject: [PATCH 02/26] python version

---
 .github/workflows/testing.yml | 2 +-
 tests/test_map_to_map.py      | 2 --
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 4b829dc..1e7f242 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3
diff --git a/tests/test_map_to_map.py b/tests/test_map_to_map.py
index 968ab07..d275259 100644
--- a/tests/test_map_to_map.py
+++ b/tests/test_map_to_map.py
@@ -1,5 +1,3 @@
 def test_pass():
     assert True
 
-def test_fail():
-    assert False
\ No newline at end of file

From 23e7323460903cda0d43ea8c180dcdd8ba4bdea5 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 15:10:16 -0400
Subject: [PATCH 03/26] should fail

---
 tests/test_map_to_map.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/test_map_to_map.py b/tests/test_map_to_map.py
index d275259..968ab07 100644
--- a/tests/test_map_to_map.py
+++ b/tests/test_map_to_map.py
@@ -1,3 +1,5 @@
 def test_pass():
     assert True
 
+def test_fail():
+    assert False
\ No newline at end of file

From 3c599ca2dab0f0b5bcd138b60c357d38a73e223f Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 15:59:27 -0400
Subject: [PATCH 04/26] unit test. should pass in about 1 min

---
 ...est_config_map_to_map_distance_matrix.yaml | 26 +++++++++++++++++++
 ....py => test_map_to_map_distance_matrix.py} |  0
 2 files changed, 26 insertions(+)
 create mode 100644 config_files/test_config_map_to_map_distance_matrix.yaml
 rename tests/{test_map_to_map.py => test_map_to_map_distance_matrix.py} (100%)

diff --git a/config_files/test_config_map_to_map_distance_matrix.yaml b/config_files/test_config_map_to_map_distance_matrix.yaml
new file mode 100644
index 0000000..0398065
--- /dev/null
+++ b/config_files/test_config_map_to_map_distance_matrix.yaml
@@ -0,0 +1,26 @@
+data:
+  n_pix: 224
+  psize: 2.146 
+  submission:
+    fname: data/submission_0.pt
+    volume_key: volumes
+    metadata_key: populations
+    label_key: id
+  ground_truth:
+    volumes: data/test_maps_gt_flat.pt 
+    metadata: data/test_metadata.csv 
+  mask: 
+    do: true
+    volume: data/mask_dilated_wide_224x224.mrc
+analysis:
+  metrics:
+    - l2
+    # - corr
+    # - bioem
+    # - fsc
+  chunk_size_submission: 80
+  chunk_size_gt: 190
+  normalize:
+    do: true
+    method: median_zscore
+output: results/test_map_to_map_distance_matrix_submission_0.pkl
\ No newline at end of file
diff --git a/tests/test_map_to_map.py b/tests/test_map_to_map_distance_matrix.py
similarity index 100%
rename from tests/test_map_to_map.py
rename to tests/test_map_to_map_distance_matrix.py

From 7952aaa0ba827735e7737a27d0d34ed739941ece Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 16:18:30 -0400
Subject: [PATCH 05/26] test data

---
 tests/data/test_metadata_2.csv                                 | 3 +++
 .../{test_map_to_map_distance_matrix.py => test_map_to_map.py} | 0
 2 files changed, 3 insertions(+)
 create mode 100644 tests/data/test_metadata_2.csv
 rename tests/{test_map_to_map_distance_matrix.py => test_map_to_map.py} (100%)

diff --git a/tests/data/test_metadata_2.csv b/tests/data/test_metadata_2.csv
new file mode 100644
index 0000000..b564400
--- /dev/null
+++ b/tests/data/test_metadata_2.csv
@@ -0,0 +1,3 @@
+index,volumes,populations_count,pc1,populations
+3238,13396.mrc,1,-231.62100638454024,2.9636654614427123e-05
+3789,30099.mrc,2,243.32448171011487,5.927330922885425e-05
diff --git a/tests/test_map_to_map_distance_matrix.py b/tests/test_map_to_map.py
similarity index 100%
rename from tests/test_map_to_map_distance_matrix.py
rename to tests/test_map_to_map.py

From 13caee8029ad02f5ce6a586f9badbffe45e4c254 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 16:39:28 -0400
Subject: [PATCH 06/26] unit test

---
 tests/test_map_to_map.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/tests/test_map_to_map.py b/tests/test_map_to_map.py
index 968ab07..7744af5 100644
--- a/tests/test_map_to_map.py
+++ b/tests/test_map_to_map.py
@@ -1,5 +1,7 @@
-def test_pass():
-    assert True
+from omegaconf import OmegaConf
+from cryo_challenge._commands import run_map2map_pipeline
 
-def test_fail():
-    assert False
\ No newline at end of file
+args = OmegaConf.create({'config': 'config_files/test_config_map_to_map_distance_matrix.yaml'})
+
+def test_run_map2map_pipeline(args):    
+    run_map2map_pipeline.main(args)
\ No newline at end of file

From 0c56ee319167aa3ed375b33cbda2c2edbf4386a4 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 16:40:00 -0400
Subject: [PATCH 07/26] path to test config

---
 tests/test_distribution_to_distribution.py | 7 +++++++
 tests/test_map_to_map.py                   | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_distribution_to_distribution.py

diff --git a/tests/test_distribution_to_distribution.py b/tests/test_distribution_to_distribution.py
new file mode 100644
index 0000000..9dcb1f0
--- /dev/null
+++ b/tests/test_distribution_to_distribution.py
@@ -0,0 +1,7 @@
+from omegaconf import OmegaConf
+from cryo_challenge._commands import run_distribution2distribution_pipeline
+
+args = OmegaConf.create({'config': 'tests/config_files/test_config_map_to_map_distance_matrix.yaml'})
+
+def test_run_distribution2distribution_pipeline(args):    
+    run_distribution2distribution_pipeline.main(args)
\ No newline at end of file
diff --git a/tests/test_map_to_map.py b/tests/test_map_to_map.py
index 7744af5..d470e21 100644
--- a/tests/test_map_to_map.py
+++ b/tests/test_map_to_map.py
@@ -1,7 +1,7 @@
 from omegaconf import OmegaConf
 from cryo_challenge._commands import run_map2map_pipeline
 
-args = OmegaConf.create({'config': 'config_files/test_config_map_to_map_distance_matrix.yaml'})
+args = OmegaConf.create({'config': 'tests/config_files/test_config_map_to_map_distance_matrix.yaml'})
 
 def test_run_map2map_pipeline(args):    
     run_map2map_pipeline.main(args)
\ No newline at end of file

From 4e12a3fe12abe569ae3615df2c0f6026692807df Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 17:30:05 -0400
Subject: [PATCH 08/26] wget from osf, test. full data

---
 .github/workflows/testing.yml                 |  6 +++++
 ...t_config_distribution_to_distribution.yaml | 12 ++++++++++
 .../config_files/test_config_map_to_map.yaml  | 23 +++++++++++++++++++
 3 files changed, 41 insertions(+)
 create mode 100644 tests/config_files/test_config_distribution_to_distribution.yaml
 create mode 100644 tests/config_files/test_config_map_to_map.yaml

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 1e7f242..65db3c0 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -27,6 +27,12 @@ jobs:
           python -m pip install --upgrade pip
           pip install .
           pip install pytest
+      - name: Get test data
+        run: |
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/submission_0.pt?download=true -O data/dataset_2_submissions/submission_0.pt
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/gt_maps_flat_float16.pt?download=true -O data/gt_maps_flat_float16.pt
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O data/metadata.csv 
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O data/mask_dilated_wide_224x224.mrc 
       - name: Test with pytest
         run: |
           pytest tests/
diff --git a/tests/config_files/test_config_distribution_to_distribution.yaml b/tests/config_files/test_config_distribution_to_distribution.yaml
new file mode 100644
index 0000000..48f2546
--- /dev/null
+++ b/tests/config_files/test_config_distribution_to_distribution.yaml
@@ -0,0 +1,12 @@
+input_fname: results/test_map_to_map_distance_matrix_submission_0.pkl
+metrics:
+  - l2
+gt_metadata_fname: data/metadata.csv
+n_replicates: 3
+n_pool_microstate: 2
+replicate_fraction: 0.9
+cvxpy_solver: ECOS
+optimal_q_kl:
+  n_iter: 100000
+  break_atol: 0.0001
+output_fname: results/test_distribution_to_distribution_submission_0.pkl
\ No newline at end of file
diff --git a/tests/config_files/test_config_map_to_map.yaml b/tests/config_files/test_config_map_to_map.yaml
new file mode 100644
index 0000000..47e5bd1
--- /dev/null
+++ b/tests/config_files/test_config_map_to_map.yaml
@@ -0,0 +1,23 @@
+data:
+  n_pix: 224
+  psize: 2.146 
+  submission:
+    fname: tests/data/dataset_2_submissions/submission_0.pt
+    volume_key: volumes
+    metadata_key: populations
+    label_key: id
+  ground_truth:
+    volumes: data/gt_maps_flat_float16.pt 
+    metadata: data/metadata.csv 
+  mask: 
+    do: true
+    volume: data/mask_dilated_wide_224x224.mrc
+analysis:
+  metrics:
+    - l2
+  chunk_size_submission: 80
+  chunk_size_gt: 190
+  normalize:
+    do: true
+    method: median_zscore
+output: tests/test_map_to_map_distance_matrix_submission_0.pkl
\ No newline at end of file

From a94d8f27589aa1b782966f209f35dc9d42a4cdcd Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 17:33:19 -0400
Subject: [PATCH 09/26] testing data

---
 .github/workflows/testing.yml                  | 4 ++--
 tests/config_files/test_config_map_to_map.yaml | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 65db3c0..352ac5f 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -30,8 +30,8 @@ jobs:
       - name: Get test data
         run: |
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/submission_0.pt?download=true -O data/dataset_2_submissions/submission_0.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/gt_maps_flat_float16.pt?download=true -O data/gt_maps_flat_float16.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O data/metadata.csv 
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/gt_maps_flat_float16.pt?download=true -O tests/data/gt_maps_flat_10.pt
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O tests/data/metadat_10a.csv 
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O data/mask_dilated_wide_224x224.mrc 
       - name: Test with pytest
         run: |
diff --git a/tests/config_files/test_config_map_to_map.yaml b/tests/config_files/test_config_map_to_map.yaml
index 47e5bd1..7a093dc 100644
--- a/tests/config_files/test_config_map_to_map.yaml
+++ b/tests/config_files/test_config_map_to_map.yaml
@@ -2,13 +2,13 @@ data:
   n_pix: 224
   psize: 2.146 
   submission:
-    fname: tests/data/dataset_2_submissions/submission_0.pt
+    fname: data/dataset_2_submissions/submission_0.pt
     volume_key: volumes
     metadata_key: populations
     label_key: id
   ground_truth:
-    volumes: data/gt_maps_flat_float16.pt 
-    metadata: data/metadata.csv 
+    volumes: tests/data/gt_maps_flat_10.pt 
+    metadata: tests/data/metadata_10.csv 
   mask: 
     do: true
     volume: data/mask_dilated_wide_224x224.mrc

From b5be9add00d7fd2ab646241f3f214437cd11d291 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 17:37:48 -0400
Subject: [PATCH 10/26] empty file for directory

---
 data/dataset_2_submissions/emptyfile.txt | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 data/dataset_2_submissions/emptyfile.txt

diff --git a/data/dataset_2_submissions/emptyfile.txt b/data/dataset_2_submissions/emptyfile.txt
new file mode 100644
index 0000000..e69de29

From 0525c74c432091e4f5e5a542437e108fa3fda735 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 17:38:08 -0400
Subject: [PATCH 11/26] name of test

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 352ac5f..b348ec5 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -27,7 +27,7 @@ jobs:
           python -m pip install --upgrade pip
           pip install .
           pip install pytest
-      - name: Get test data
+      - name: Get test data from OSF
         run: |
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/submission_0.pt?download=true -O data/dataset_2_submissions/submission_0.pt
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/gt_maps_flat_float16.pt?download=true -O tests/data/gt_maps_flat_10.pt

From ee5bc6453ae7a7b9bc85d622c6d1d9318bf37418 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 17:40:40 -0400
Subject: [PATCH 12/26] remove file. can mkdir in github workflow runner

---
 data/dataset_2_submissions/emptyfile.txt | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 data/dataset_2_submissions/emptyfile.txt

diff --git a/data/dataset_2_submissions/emptyfile.txt b/data/dataset_2_submissions/emptyfile.txt
deleted file mode 100644
index e69de29..0000000

From 59a283b110b069b97d7b7668d98beb53f18d0f69 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 17:48:42 -0400
Subject: [PATCH 13/26] paths to osf files and pip caching

---
 .github/workflows/testing.yml                 | 14 +++++++---
 ...est_config_map_to_map_distance_matrix.yaml | 26 -------------------
 2 files changed, 11 insertions(+), 29 deletions(-)
 delete mode 100644 config_files/test_config_map_to_map_distance_matrix.yaml

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index b348ec5..e7e472d 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -22,6 +22,13 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Cache pip wheels
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -29,10 +36,11 @@ jobs:
           pip install pytest
       - name: Get test data from OSF
         run: |
+          mkdir data/dataset_2_submissions
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/submission_0.pt?download=true -O data/dataset_2_submissions/submission_0.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/gt_maps_flat_float16.pt?download=true -O tests/data/gt_maps_flat_10.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O tests/data/metadat_10a.csv 
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O data/mask_dilated_wide_224x224.mrc 
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/gt_maps_flat_10.pt?download=true -O tests/data/gt_maps_flat_10.pt
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata_10.csv?download=true -O tests/data/metadata_10.csv 
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O data/mask_dilated_wide_224x224.mrc 
       - name: Test with pytest
         run: |
           pytest tests/
diff --git a/config_files/test_config_map_to_map_distance_matrix.yaml b/config_files/test_config_map_to_map_distance_matrix.yaml
deleted file mode 100644
index 0398065..0000000
--- a/config_files/test_config_map_to_map_distance_matrix.yaml
+++ /dev/null
@@ -1,26 +0,0 @@
-data:
-  n_pix: 224
-  psize: 2.146 
-  submission:
-    fname: data/submission_0.pt
-    volume_key: volumes
-    metadata_key: populations
-    label_key: id
-  ground_truth:
-    volumes: data/test_maps_gt_flat.pt 
-    metadata: data/test_metadata.csv 
-  mask: 
-    do: true
-    volume: data/mask_dilated_wide_224x224.mrc
-analysis:
-  metrics:
-    - l2
-    # - corr
-    # - bioem
-    # - fsc
-  chunk_size_submission: 80
-  chunk_size_gt: 190
-  normalize:
-    do: true
-    method: median_zscore
-output: results/test_map_to_map_distance_matrix_submission_0.pkl
\ No newline at end of file

From 78d7d3b25552008fe584c45a6ffa6fdcf02ca163 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 17:56:09 -0400
Subject: [PATCH 14/26] =?UTF-8?q?mkdir:=20cannot=20create=20directory=20?=
 =?UTF-8?q?=E2=80=98data/dataset=5F2=5Fsubmissions=E2=80=99:=20No=20such?=
 =?UTF-8?q?=20file=20or=20directory?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index e7e472d..773cb66 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -36,7 +36,7 @@ jobs:
           pip install pytest
       - name: Get test data from OSF
         run: |
-          mkdir data/dataset_2_submissions
+          mkdir -p data/dataset_2_submissions tests/data/
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/submission_0.pt?download=true -O data/dataset_2_submissions/submission_0.pt
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/gt_maps_flat_10.pt?download=true -O tests/data/gt_maps_flat_10.pt
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata_10.csv?download=true -O tests/data/metadata_10.csv 

From d6535451d4fa20f59e2aa690f4180f7561d10bfe Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 18:12:53 -0400
Subject: [PATCH 15/26] local pytest passing. osf paths updated.

---
 .github/workflows/testing.yml                               | 6 +++---
 .../test_config_distribution_to_distribution.yaml           | 4 ++--
 tests/config_files/test_config_map_to_map.yaml              | 6 +++---
 tests/test_distribution_to_distribution.py                  | 4 ++--
 tests/test_map_to_map.py                                    | 4 ++--
 5 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 773cb66..d476ee8 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -36,10 +36,10 @@ jobs:
           pip install pytest
       - name: Get test data from OSF
         run: |
-          mkdir -p data/dataset_2_submissions tests/data/
+          mkdir -p data/dataset_2_submissions tests/data/ tests/results
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/submission_0.pt?download=true -O data/dataset_2_submissions/submission_0.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/gt_maps_flat_10.pt?download=true -O tests/data/gt_maps_flat_10.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata_10.csv?download=true -O tests/data/metadata_10.csv 
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/gt_maps_flat_10.pt
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_metadata_10.csv?download=true -O tests/data/metadata_10.csv 
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O data/mask_dilated_wide_224x224.mrc 
       - name: Test with pytest
         run: |
diff --git a/tests/config_files/test_config_distribution_to_distribution.yaml b/tests/config_files/test_config_distribution_to_distribution.yaml
index 48f2546..9359e58 100644
--- a/tests/config_files/test_config_distribution_to_distribution.yaml
+++ b/tests/config_files/test_config_distribution_to_distribution.yaml
@@ -1,7 +1,7 @@
-input_fname: results/test_map_to_map_distance_matrix_submission_0.pkl
+input_fname: tests/results/test_map_to_map_distance_matrix_submission_0.pkl
 metrics:
   - l2
-gt_metadata_fname: data/metadata.csv
+gt_metadata_fname: tests/data/test_metadata_10.csv
 n_replicates: 3
 n_pool_microstate: 2
 replicate_fraction: 0.9
diff --git a/tests/config_files/test_config_map_to_map.yaml b/tests/config_files/test_config_map_to_map.yaml
index 7a093dc..2e7af67 100644
--- a/tests/config_files/test_config_map_to_map.yaml
+++ b/tests/config_files/test_config_map_to_map.yaml
@@ -7,8 +7,8 @@ data:
     metadata_key: populations
     label_key: id
   ground_truth:
-    volumes: tests/data/gt_maps_flat_10.pt 
-    metadata: tests/data/metadata_10.csv 
+    volumes: tests/data/test_maps_gt_flat_10.pt 
+    metadata: tests/data/test_metadata_10.csv 
   mask: 
     do: true
     volume: data/mask_dilated_wide_224x224.mrc
@@ -20,4 +20,4 @@ analysis:
   normalize:
     do: true
     method: median_zscore
-output: tests/test_map_to_map_distance_matrix_submission_0.pkl
\ No newline at end of file
+output: tests/results/test_map_to_map_distance_matrix_submission_0.pkl
\ No newline at end of file
diff --git a/tests/test_distribution_to_distribution.py b/tests/test_distribution_to_distribution.py
index 9dcb1f0..d9c340b 100644
--- a/tests/test_distribution_to_distribution.py
+++ b/tests/test_distribution_to_distribution.py
@@ -1,7 +1,7 @@
 from omegaconf import OmegaConf
 from cryo_challenge._commands import run_distribution2distribution_pipeline
 
-args = OmegaConf.create({'config': 'tests/config_files/test_config_map_to_map_distance_matrix.yaml'})
 
-def test_run_distribution2distribution_pipeline(args):    
+def test_run_distribution2distribution_pipeline():   
+    args = OmegaConf.create({'config': 'tests/config_files/test_config_distribution_to_distribution.yaml'})
     run_distribution2distribution_pipeline.main(args)
\ No newline at end of file
diff --git a/tests/test_map_to_map.py b/tests/test_map_to_map.py
index d470e21..c782a8c 100644
--- a/tests/test_map_to_map.py
+++ b/tests/test_map_to_map.py
@@ -1,7 +1,7 @@
 from omegaconf import OmegaConf
 from cryo_challenge._commands import run_map2map_pipeline
 
-args = OmegaConf.create({'config': 'tests/config_files/test_config_map_to_map_distance_matrix.yaml'})
 
-def test_run_map2map_pipeline(args):    
+def test_run_map2map_pipeline():    
+    args = OmegaConf.create({'config': 'tests/config_files/test_config_map_to_map.yaml'})
     run_map2map_pipeline.main(args)
\ No newline at end of file

From 76689e9a62463c999d62967a0718c1d4b94dfd7c Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 18:24:06 -0400
Subject: [PATCH 16/26] omegaconf dependency

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index d476ee8..2c20784 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -33,7 +33,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install .
-          pip install pytest
+          pip install pytest omegaconf
       - name: Get test data from OSF
         run: |
           mkdir -p data/dataset_2_submissions tests/data/ tests/results

From 48ab7750b05121d6dd94e68cb108e8300a4f5d36 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 20:29:37 -0400
Subject: [PATCH 17/26] test submission with 8 volumes

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 2c20784..9102a97 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -36,8 +36,8 @@ jobs:
           pip install pytest omegaconf
       - name: Get test data from OSF
         run: |
-          mkdir -p data/dataset_2_submissions tests/data/ tests/results
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/submission_0.pt?download=true -O data/dataset_2_submissions/submission_0.pt
+          mkdir -p data/dataset_2_submissions tests/data/dataset_2_submissions tests/results
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/test_submission_0_n8.pt?download=true -O tests/data/dataset_2_submissions/test_submission_0_n8.pt
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/gt_maps_flat_10.pt
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_metadata_10.csv?download=true -O tests/data/metadata_10.csv 
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O data/mask_dilated_wide_224x224.mrc 

From 5b2e576277dbd55cc2c90c908f4355bb01931192 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 20:30:22 -0400
Subject: [PATCH 18/26] path

---
 tests/config_files/test_config_map_to_map.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/config_files/test_config_map_to_map.yaml b/tests/config_files/test_config_map_to_map.yaml
index 2e7af67..eed5fb0 100644
--- a/tests/config_files/test_config_map_to_map.yaml
+++ b/tests/config_files/test_config_map_to_map.yaml
@@ -2,7 +2,7 @@ data:
   n_pix: 224
   psize: 2.146 
   submission:
-    fname: data/dataset_2_submissions/submission_0.pt
+    fname: tests/data/dataset_2_submissions/test_submission_0_n8.pt
     volume_key: volumes
     metadata_key: populations
     label_key: id

From a8a8a95e2bdb1cb2801a5e6b4d95516f4162a633 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 20:35:23 -0400
Subject: [PATCH 19/26] paths

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 9102a97..c1da099 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -38,8 +38,8 @@ jobs:
         run: |
           mkdir -p data/dataset_2_submissions tests/data/dataset_2_submissions tests/results
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/test_submission_0_n8.pt?download=true -O tests/data/dataset_2_submissions/test_submission_0_n8.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/gt_maps_flat_10.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_metadata_10.csv?download=true -O tests/data/metadata_10.csv 
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/test_maps_gt_flat_10.pt
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_metadata_10.csv?download=true -O tests/data/test_metadata_10.csv 
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O data/mask_dilated_wide_224x224.mrc 
       - name: Test with pytest
         run: |

From d80124593166b8213d367c2cafe5c85f1e631138 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 20:55:35 -0400
Subject: [PATCH 20/26] order of tests

---
 .github/workflows/testing.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index c1da099..2b67b37 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -43,4 +43,5 @@ jobs:
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O data/mask_dilated_wide_224x224.mrc 
       - name: Test with pytest
         run: |
-          pytest tests/
+          pytest tests/test_map_to_map.py
+          pytest tests/test_distribution_to_distribution.py 

From 8d905e6e94a2e03b8caf5195c6185ae9554f9c16 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 21:03:44 -0400
Subject: [PATCH 21/26] script for getting osf data

---
 tests/scripts/fetch_test_data.sh | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 tests/scripts/fetch_test_data.sh

diff --git a/tests/scripts/fetch_test_data.sh b/tests/scripts/fetch_test_data.sh
new file mode 100644
index 0000000..740d895
--- /dev/null
+++ b/tests/scripts/fetch_test_data.sh
@@ -0,0 +1,5 @@
+mkdir -p data/dataset_2_submissions tests/data/dataset_2_submissions tests/results
+wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/test_submission_0_n8.pt?download=true -O tests/data/dataset_2_submissions/test_submission_0_n8.pt
+wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/test_maps_gt_flat_10.pt
+wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_metadata_10.csv?download=true -O tests/data/test_metadata_10.csv 
+wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O data/mask_dilated_wide_224x224.mrc 
\ No newline at end of file

From 9afc6e642ef45f4aa84bb97d6bdedde221ab8706 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 21:11:05 -0400
Subject: [PATCH 22/26] script to download

---
 .github/workflows/testing.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 2b67b37..327e80f 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -36,11 +36,7 @@ jobs:
           pip install pytest omegaconf
       - name: Get test data from OSF
         run: |
-          mkdir -p data/dataset_2_submissions tests/data/dataset_2_submissions tests/results
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/test_submission_0_n8.pt?download=true -O tests/data/dataset_2_submissions/test_submission_0_n8.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/test_maps_gt_flat_10.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_metadata_10.csv?download=true -O tests/data/test_metadata_10.csv 
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O data/mask_dilated_wide_224x224.mrc 
+          sh tests/scripts/fetch_test_data.sh
       - name: Test with pytest
         run: |
           pytest tests/test_map_to_map.py

From 969c46b831df4c605e56d87aa89401bd13533338 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 21:58:50 -0400
Subject: [PATCH 23/26] cache data

---
 .github/workflows/testing.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 327e80f..c0cd322 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -25,8 +25,10 @@ jobs:
       - name: Cache pip wheels
         uses: actions/cache@v3
         with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+          path: |
+            ~/.cache/pip
+            tests/data
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml', '**/tests/scripts/fetch_test_data.sh') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Install dependencies

From 52e53ad43480dab7269b7304cbfee5632c09c1d4 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 21:59:45 -0400
Subject: [PATCH 24/26] cache data

---
 .github/workflows/testing.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index c0cd322..228e04a 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -28,6 +28,7 @@ jobs:
           path: |
             ~/.cache/pip
             tests/data
+            data
           key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml', '**/tests/scripts/fetch_test_data.sh') }}
           restore-keys: |
             ${{ runner.os }}-pip-

From 4aed02c944c21064731f7fffe078f2be20bde271 Mon Sep 17 00:00:00 2001
From: Geoffrey Woollard <geoffwoollard@gmail.com>
Date: Thu, 20 Jun 2024 22:05:12 -0400
Subject: [PATCH 25/26] cache data

---
 .github/workflows/testing.yml | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 228e04a..277ad1a 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -1,6 +1,6 @@
-# GHA workflow for running tests. 
+# GHA workflow for running tests.
 #
-# Largely taken from 
+# Largely taken from
 # https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 # Please check the link for more detailed instructions
 
@@ -18,11 +18,14 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+      
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache pip wheels
+          
+      - name: Cache dependencies and test data
+        id: cache
         uses: actions/cache@v3
         with:
           path: |
@@ -32,15 +35,19 @@ jobs:
           key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml', '**/tests/scripts/fetch_test_data.sh') }}
           restore-keys: |
             ${{ runner.os }}-pip-
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install .
           pip install pytest omegaconf
+          
       - name: Get test data from OSF
+        if: steps.cache.outputs.cache-hit != 'true'
         run: |
           sh tests/scripts/fetch_test_data.sh
+          
       - name: Test with pytest
         run: |
           pytest tests/test_map_to_map.py
-          pytest tests/test_distribution_to_distribution.py 
+          pytest tests/test_distribution_to_distribution.py

From e9e0532d998b785e5db2ece11c29a83d0fafb7b1 Mon Sep 17 00:00:00 2001
From: DavidHerreros <david.herreroscalero@gmail.com>
Date: Mon, 24 Jun 2024 10:06:29 +0200
Subject: [PATCH 26/26] Adding omegaconf to "dev" dependencies to allow running
 the tests locally

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index cf03973..85e73d5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,7 +58,8 @@ dev = [
   "pytest",
   "mypy",
   "pre-commit",
-  "ruff"
+  "ruff",
+  "omegaconf"
 ]
 
 [project.urls]