Update format

.github/workflows/draft-pdf.yml

@@ -11,14 +11,10 @@ jobs:
         uses: neurolibre/neurolibre-draft-action@master
         with:
           journal: neurolibre
-          # This should be the path to the paper within your repo.
           paper-path: paper.md
       - name: Upload
         uses: actions/upload-artifact@v4
         with:
           name: paper
-          # This is the output path where Pandoc will write the compiled
-          # PDF. Note, this should be the same directory as the input
-          # paper.md
           path: paper.pdf
 

.gitignore

@@ -1,29 +1,35 @@
-content/Sections/Dataset/Data_Boulder/data.zip
-content/Sections/Dataset/Data_Ottawa/data.zip
-
-content/Sections/Results/Geometric/Confidence/*
-content/Sections/Results/Geometric/Density/*
-content/Sections/Results/Geometric/Confidence.pdf
-content/Sections/Results/Uniform/Confidence/*
-content/Sections/Results/Uniform/Density/*
-content/Sections/Results/Uniform/g2/*
-content/Sections/Results/Uniform/Confidence.pdf
-content/Sections/Results/Large/Confidence/*
-content/Sections/Results/Large/Density/*
-content/Sections/Results/Large/Confidence.pdf
-
-!content/Sections/Results/Geometric/Confidence/.gitkeep
-!content/Sections/Results/Geometric/Density/.gitkeep
-!content/Sections/Results/Uniform/Confidence/.gitkeep
-!content/Sections/Results/Uniform/Density/.gitkeep
-!content/Sections/Results/Uniform/g2/.gitkeep
-!content/Sections/Results/Large/Confidence/.gitkeep
-!content/Sections/Results/Large/Density/.gitkeep
-
-!content/Sections/Results/Geometric/.gitkeep
-!content/Sections/Results/Uniform/.gitkeep
-!content/Sections/Results/Large/.gitkeep
-
+content/Dataset/Data_Boulder/data.zip
+content/Dataset/Data_Ottawa/data.zip
+
+content/Results/Geometric/Confidence/*
+content/Results/Geometric/Density/*
+content/Results/Geometric/Confidence.pdf
+content/Results/Uniform/Confidence/*
+content/Results/Uniform/Density/*
+content/Results/Uniform/g2/*
+content/Results/Uniform/Confidence.pdf
+content/Results/Large/Confidence/*
+content/Results/Large/Density/*
+content/Results/Large/Confidence.pdf
+content/Results/Demo/Confidence/*
+content/Results/Demo/Density/*
+
+!content/Results/Geometric/Confidence/.gitkeep
+!content/Results/Geometric/Density/.gitkeep
+!content/Results/Uniform/Confidence/.gitkeep
+!content/Results/Uniform/Density/.gitkeep
+!content/Results/Uniform/g2/.gitkeep
+!content/Results/Large/Confidence/.gitkeep
+!content/Results/Large/Density/.gitkeep
+!content/Results/Demo/Confidence/.gitkeep
+!content/Results/Demo/Density/.gitkeep
+
+!content/Results/Geometric/.gitkeep
+!content/Results/Uniform/.gitkeep
+!content/Results/Large/.gitkeep
+!content/Results/Demo/.gitkeep
+
+_build/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -188,3 +194,6 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
+
+# MyST build outputs
+_build

binder/data_requirement.json

@@ -1,12 +1,12 @@
 {
 "Boulder" : {
    "src": "10.5281/zenodo.14101974",
-   "dst": "../data",
+   "dst": "../Dataset/Data_Boulder",
    "projectName": "photon-number-classification/data_boulder"
 },
 "Ottawa" : {
    "src": "10.5281/zenodo.14042152",
-   "dst": "../data",
+   "dst": "../Dataset/Data_Ottawa",
    "projectName": "photon-number-classification/data_ottawa"
 }
 }

binder/requirements.txt

@@ -9,4 +9,18 @@ scipy==1.14.1
 seaborn==0.13.2
 torch==2.5.1
 tqdm==4.67.1
-umap_learn==0.5.7
+umap_learn==0.5.7
+
+# --extra-index-url https://download.pytorch.org/whl/cpu
+# adjustText==1.3.0
+# matplotlib==3.9.3
+# numpy==2.1.3
+# polars==1.16.0
+# pynndescent==0.5.13
+# pytorch_lightning==2.4.0
+# scikit_learn==1.5.2
+# scipy==1.14.1
+# seaborn==0.13.2
+# torch==2.5.1+cpu
+# tqdm==4.67.1
+# umap_learn==0.5.7