Skip to content

Commit 22cfb7c

Browse files
MaximLippeveldMaximLippeveld
committed
Documentation update
1 parent f0cf5d4 commit 22cfb7c

25 files changed

+205
-136
lines changed

‎README.md

Lines changed: 10 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -8,19 +8,26 @@ Scalable Cytometry Image Processing (SCIP) is an open-source tool that implement
88
an image processing pipeline on top of Dask, a distributed computing framework written in Python.
99
SCIP performs normalization, image segmentation and masking, and feature extraction.
1010

11-
Check the docs for installation and usage instructions.
11+
Check the [docs](https://readthedocs.org/projects/scalable-cytometry-image-processing) for
12+
installation and usage instructions, and API documentation.
1213

1314
## Development
1415

1516
### Generating documentation
17+
18+
For publishing online:
1619
```
1720
cd docs
18-
rm -r source/generated/
19-
sphinx-apidoc -f -T -o source/generated/ ../src/scip
2021
make clean
2122
make html
2223
```
2324

25+
For development with live reloading:
26+
```
27+
cd docs
28+
make livehtml
29+
```
30+
2431
### Generate release changelog
2532
```
2633
git log v{previous version tag}..HEAD --oneline | xclip -sel clip

‎docs/Makefile

Lines changed: 10 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@
55
# from the environment for the first two.
66
SPHINXOPTS ?=
77
SPHINXBUILD ?= sphinx-build
8+
SPHINXAPIDOC = sphinx-apidoc
89
SOURCEDIR = source
910
BUILDDIR = build
1011

@@ -14,10 +15,14 @@ help:
1415

1516
.PHONY: help Makefile
1617

17-
# Catch-all target: route all unknown targets to Sphinx using the new
18-
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
19-
%: Makefile
18+
html: api
2019
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
2120

22-
livehtml:
23-
sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
21+
api:
22+
@$(SPHINXAPIDOC) -f -T -M -o "$(SOURCEDIR)/generated" ../src/scip
23+
24+
livehtml: api
25+
sphinx-autobuild --watch ../src "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
26+
27+
clean:
28+
rm -r "$(SOURCEDIR)/generated" $(BUILDDIR)

‎docs/source/conf.py

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -28,9 +28,7 @@
2828
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
2929
# ones.
3030
extensions = [
31-
'sphinx.ext.autodoc',
3231
'sphinx.ext.napoleon',
33-
'sphinx.ext.autosummary',
3432
'sphinx_copybutton'
3533
]
3634

‎docs/source/generated/scip.export.rst

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,11 @@
11
scip.export package
22
===================
33

4+
.. automodule:: scip.export
5+
:members:
6+
:undoc-members:
7+
:show-inheritance:
8+
49
Submodules
510
----------
611

@@ -19,11 +24,3 @@ scip.export.parquet module
1924
:members:
2025
:undoc-members:
2126
:show-inheritance:
22-
23-
Module contents
24-
---------------
25-
26-
.. automodule:: scip.export
27-
:members:
28-
:undoc-members:
29-
:show-inheritance:

‎docs/source/generated/scip.features.rst

Lines changed: 13 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,11 @@
11
scip.features package
22
=====================
33

4+
.. automodule:: scip.features
5+
:members:
6+
:undoc-members:
7+
:show-inheritance:
8+
49
Submodules
510
----------
611

@@ -20,6 +25,14 @@ scip.features.intensity module
2025
:undoc-members:
2126
:show-inheritance:
2227

28+
scip.features.raw\_intensity module
29+
-----------------------------------
30+
31+
.. automodule:: scip.features.raw_intensity
32+
:members:
33+
:undoc-members:
34+
:show-inheritance:
35+
2336
scip.features.shape module
2437
--------------------------
2538

@@ -35,11 +48,3 @@ scip.features.texture module
3548
:members:
3649
:undoc-members:
3750
:show-inheritance:
38-
39-
Module contents
40-
---------------
41-
42-
.. automodule:: scip.features
43-
:members:
44-
:undoc-members:
45-
:show-inheritance:

‎docs/source/generated/scip.filter.rst

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,11 @@
11
scip.filter package
22
===================
33

4+
.. automodule:: scip.filter
5+
:members:
6+
:undoc-members:
7+
:show-inheritance:
8+
49
Submodules
510
----------
611

@@ -11,11 +16,3 @@ scip.filter.threshold module
1116
:members:
1217
:undoc-members:
1318
:show-inheritance:
14-
15-
Module contents
16-
---------------
17-
18-
.. automodule:: scip.filter
19-
:members:
20-
:undoc-members:
21-
:show-inheritance:

‎docs/source/generated/scip.illumination_correction.rst

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,11 @@
11
scip.illumination\_correction package
22
=====================================
33

4+
.. automodule:: scip.illumination_correction
5+
:members:
6+
:undoc-members:
7+
:show-inheritance:
8+
49
Submodules
510
----------
611

@@ -11,11 +16,3 @@ scip.illumination\_correction.jones\_2006 module
1116
:members:
1217
:undoc-members:
1318
:show-inheritance:
14-
15-
Module contents
16-
---------------
17-
18-
.. automodule:: scip.illumination_correction
19-
:members:
20-
:undoc-members:
21-
:show-inheritance:

‎docs/source/generated/scip.loading.rst

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,11 @@
11
scip.loading package
22
====================
33

4+
.. automodule:: scip.loading
5+
:members:
6+
:undoc-members:
7+
:show-inheritance:
8+
49
Submodules
510
----------
611

@@ -43,11 +48,3 @@ scip.loading.zarr module
4348
:members:
4449
:undoc-members:
4550
:show-inheritance:
46-
47-
Module contents
48-
---------------
49-
50-
.. automodule:: scip.loading
51-
:members:
52-
:undoc-members:
53-
:show-inheritance:

‎docs/source/generated/scip.masking.filters.rst

Lines changed: 34 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,34 @@
1+
scip.masking.filters package
2+
============================
3+
4+
.. automodule:: scip.masking.filters
5+
:members:
6+
:undoc-members:
7+
:show-inheritance:
8+
9+
Submodules
10+
----------
11+
12+
scip.masking.filters.normaltest module
13+
--------------------------------------
14+
15+
.. automodule:: scip.masking.filters.normaltest
16+
:members:
17+
:undoc-members:
18+
:show-inheritance:
19+
20+
scip.masking.filters.std module
21+
-------------------------------
22+
23+
.. automodule:: scip.masking.filters.std
24+
:members:
25+
:undoc-members:
26+
:show-inheritance:
27+
28+
scip.masking.filters.value\_range module
29+
----------------------------------------
30+
31+
.. automodule:: scip.masking.filters.value_range
32+
:members:
33+
:undoc-members:
34+
:show-inheritance:

‎docs/source/generated/scip.masking.rst

Lines changed: 27 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,19 @@
11
scip.masking package
22
====================
33

4+
.. automodule:: scip.masking
5+
:members:
6+
:undoc-members:
7+
:show-inheritance:
8+
9+
Subpackages
10+
-----------
11+
12+
.. toctree::
13+
:maxdepth: 4
14+
15+
scip.masking.filters
16+
417
Submodules
518
----------
619

@@ -12,42 +25,42 @@ scip.masking.circle module
1225
:undoc-members:
1326
:show-inheritance:
1427

15-
scip.masking.sobel module
16-
-------------------------
28+
scip.masking.li module
29+
----------------------
1730

18-
.. automodule:: scip.masking.sobel
31+
.. automodule:: scip.masking.li
1932
:members:
2033
:undoc-members:
2134
:show-inheritance:
2235

23-
scip.masking.spot module
36+
scip.masking.otsu module
2437
------------------------
2538

26-
.. automodule:: scip.masking.spot
39+
.. automodule:: scip.masking.otsu
2740
:members:
2841
:undoc-members:
2942
:show-inheritance:
3043

31-
scip.masking.threshold module
32-
-----------------------------
44+
scip.masking.sobel module
45+
-------------------------
3346

34-
.. automodule:: scip.masking.threshold
47+
.. automodule:: scip.masking.sobel
3548
:members:
3649
:undoc-members:
3750
:show-inheritance:
3851

39-
scip.masking.watershed module
40-
-----------------------------
52+
scip.masking.spot module
53+
------------------------
4154

42-
.. automodule:: scip.masking.watershed
55+
.. automodule:: scip.masking.spot
4356
:members:
4457
:undoc-members:
4558
:show-inheritance:
4659

47-
Module contents
48-
---------------
60+
scip.masking.watershed module
61+
-----------------------------
4962

50-
.. automodule:: scip.masking
63+
.. automodule:: scip.masking.watershed
5164
:members:
5265
:undoc-members:
5366
:show-inheritance:

0 commit comments

Comments
 (0)