Fix issues in doc

Author: constantinpape

.github/workflows/build_docs.yaml

@@ -37,8 +37,8 @@ jobs:
       run: pip install -e .
 
     - name: Generate Documentation
-      shell: bash -l {0} 
-      run: pdoc synaptic_reconstruction -o doc/
+      shell: bash -l {0}
+      run: pdoc synaptic_reconstruction -d google -o doc/
 
     - name: Verify Documentation Output
       run: ls -la doc/
@@ -68,6 +68,6 @@ jobs:
 
       - name: Deploy to GiHub Pages
         uses: actions/deploy-pages@v4
-        # with: 
+        # with:
         #   artifact_name: documentation
 

build_doc.py

@@ -1,46 +1,16 @@
 import argparse
-import glob
-import os
-import warnings
-
 from subprocess import run
 
 
-def check_docs_completeness():
-    """@private
-    All markdown and RST documentation files **SHOULD** be included in the module
-    docstring at micro_sam/__init__.py
-    """
-    import micro_sam
-
-    # We don't search in subfolders anymore, to allow putting additional documentation
-    # (e.g. for bioimage.io mdoels) that should not be included in the main documentation here.
-    markdown_doc_files = glob.glob("doc/*.md", recursive=True)
-    rst_doc_files = glob.glob("doc/*.rst", recursive=True)
-    all_doc_files = markdown_doc_files + rst_doc_files
-    missing_from_docs = [f for f in all_doc_files if os.path.basename(f) not in micro_sam.__doc__]
-    if len(missing_from_docs) > 0:
-        warnings.warn(
-            "Documentation files missing! Please add include statements "
-            "to the docstring in micro_sam/__init__.py for every file, eg:"
-            "'.. include:: ../doc/filename.md'. "
-            "List of missing files: "
-            f"{missing_from_docs}"
-        )
-
-
 if __name__ == "__main__":
-    check_docs_completeness()
-
     parser = argparse.ArgumentParser()
     parser.add_argument("--out", "-o", action="store_true")
     args = parser.parse_args()
 
-    logo_url = "https://raw.githubusercontent.com/computational-cell-analytics/micro-sam/master/doc/logo/logo_and_text.png"
-    cmd = ["pdoc", "--docformat", "google", "--logo", logo_url]
+    cmd = ["pdoc", "--docformat", "google"]
 
     if args.out:
         cmd.extend(["--out", "tmp/"])
-    cmd.append("micro_sam")
+    cmd.append("synaptic_reconstruction")
 
-    run(cmd)
+    run(cmd)

doc/start_page.md

@@ -3,10 +3,11 @@
 SynapseNet is a tool for automatic segmentation and analysis of synapses in electron micrographs.
 It provides deep neural networks for:
 - Synaptic vesicle segmentation in ssTEM (2d data) and (cryo-)electron tomography (3d data)
-- Active zone membrane segmentation in electron tomography
-- Mitochondrion segmentation in electron tomography
-- Synaptic compartment segmentation in electron tomography
-- Synaptic ribbon and pre-synaptic density segmentation for ribbon synapses in electron tomography
+- Active zone membrane segmentation in electron tomography.
+- Mitochondrion segmentation in electron tomography.
+- Synaptic compartment segmentation in electron tomography.
+- Synaptic ribbon and pre-synaptic density segmentation for ribbon synapses in electron tomography.
+
 It also offers functionality for quantifying synaptic ultrastructure based on segmentation results, for example by measuring vesicle or structure morphology, measuring distances between vesicles and structures, or assigning vesicles into different pools.
 SynapseNet mainly targets electron tomography, but can also be appled to other types of electron microscopy,
 especially throught the [domain adaptation](domain-adaptation) functionality.