Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

server refactor #1140

Merged
merged 34 commits into from
Feb 19, 2020
Merged
Show file tree
Hide file tree
Changes from 29 commits
Commits
Show all changes
34 commits
Select commit Hold shift + click to select a range
3a84ddc
refactor server, part 1 (#1116)
Jan 17, 2020
422b6d1
pin anndata to 0.6.22post1 (#1122)
Jan 22, 2020
13fde03
centroid labels (#872)
seve Jan 22, 2020
e5eecad
refactor server, part 1 (#1116)
Jan 17, 2020
3068d4e
server refactor, part 2
Jan 21, 2020
c4d0d1e
remove backend native prototype (#1104)
Jan 23, 2020
0f8b35b
refactor server, add tiledb (#1116)
Jan 27, 2020
35d826b
server refactor, code reuse between scanpy and tiledb (#1116)
Jan 28, 2020
209749d
Merge branch 'master' into refactor
Jan 29, 2020
3b192ff
refactor server, simplify config and schema
Jan 30, 2020
267ce32
refactor server, simplify config and schema (#1116)
Jan 30, 2020
260b2f2
server refactor, add in the multi dataset app (#1116)
Jan 31, 2020
df7eb5c
add missing tiledb files for the example dataset (#1106)
Feb 1, 2020
fbbe16a
server refactor, fix annotations for tiledb engine (#1116)
Feb 2, 2020
15619db
server refactor, bump numpy version (#1116)
Feb 2, 2020
6792a66
Fix use of filters for tiledb multi_index
Feb 4, 2020
526c4c7
Use cxg as the suffix for tiledb datasets
Feb 4, 2020
376094c
Use consistent naming for the data adators.
Feb 4, 2020
5c08788
Remove dead code
Feb 4, 2020
57fbcee
refactor the app_single and app_multi into a single app
Feb 5, 2020
d2a0622
Add a cache for matrix datasets (#1116)
Feb 6, 2020
07dc1ac
small fixes from previous patch
Feb 6, 2020
523c4e6
various fixes from code review (#1116)
Feb 7, 2020
87d91ca
Fixes from the review comments
Feb 12, 2020
ee25651
Merge branch 'master' of https://github.com/chanzuckerberg/cellxgene …
Feb 12, 2020
29d8e24
Renaming, scanpy -> anndata (#1116)
Feb 12, 2020
3ac970c
server refactor, simplfy the index route (#1116)
Feb 12, 2020
4ec4fa3
server refactor, consistent use of DatasetAccessError exception (#1116)
Feb 12, 2020
a3a257f
server refactor, rename TiledbAdaptor to CxgAdaptor (#1116)
Feb 12, 2020
b54f391
Add support for s3 datapaths and dataroots (#1116)
Feb 13, 2020
21d0306
server refactor, fix bugs from review (#1116)
Feb 18, 2020
12f518b
Merge branch 'master' of https://github.com/chanzuckerberg/cellxgene …
Feb 18, 2020
3a3352d
server refactor, fix bug with schema (#1116)
Feb 19, 2020
10d28af
Merge branch 'master' of https://github.com/chanzuckerberg/cellxgene …
Feb 19, 2020
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
12 changes: 6 additions & 6 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -17,12 +17,12 @@ venv/
cellxgene/

# client build
server/app/web/static/css/
server/app/web/static/img/
server/app/web/static/media/
server/app/web/static/fonts/
server/app/web/static/js/
server/app/web/templates/index\.html
server/common/web/static/css/
server/common/web/static/img/
server/common/web/static/media/
server/common/web/static/fonts/
server/common/web/static/js/
server/common/web/templates/index\.html

# Jupyter Notebook
.ipynb_checkpoints
Expand Down
4 changes: 2 additions & 2 deletions MANIFEST.in
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
recursive-include server/app/web/templates *
recursive-include server/app/web/static *
recursive-include server/common/web/templates *
recursive-include server/common/web/static *

include server/requirements.txt
include server/requirements-prepare.txt
57 changes: 13 additions & 44 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -33,24 +33,24 @@ build-client:
build-cli: build-client
git ls-files server/ | cpio -pdm $(BUILDDIR)
cp -r client/build/ $(CLIENTBUILD)
mkdir -p $(SERVERBUILD)/app/web/static/img
mkdir -p $(SERVERBUILD)/app/web/templates/
cp $(CLIENTBUILD)/index.html $(SERVERBUILD)/app/web/templates/
cp -r $(CLIENTBUILD)/static $(SERVERBUILD)/app/web/
cp $(CLIENTBUILD)/favicon.png $(SERVERBUILD)/app/web/static/img
cp $(CLIENTBUILD)/service-worker.js $(SERVERBUILD)/app/web/static/js/
mkdir -p $(SERVERBUILD)/common/web/static/img
mkdir -p $(SERVERBUILD)/common/web/templates/
cp $(CLIENTBUILD)/index.html $(SERVERBUILD)/common/web/templates/
cp -r $(CLIENTBUILD)/static $(SERVERBUILD)/common/web/
cp $(CLIENTBUILD)/favicon.png $(SERVERBUILD)/common/web/static/img
cp $(CLIENTBUILD)/service-worker.js $(SERVERBUILD)/common/web/static/js/
cp MANIFEST.in README.md setup.cfg setup.py $(BUILDDIR)

# If you are actively developing in the server folder use this, dirties the source tree
.PHONY: build-for-server-dev
build-for-server-dev: clean-server build-client
mkdir -p server/app/web/static/img
mkdir -p server/app/web/static/js
mkdir -p server/app/web/templates/
cp client/build/index.html server/app/web/templates/
cp -r client/build/static server/app/web/
cp client/build/favicon.png server/app/web/static/img
cp client/build/service-worker.js server/app/web/static/js/
mkdir -p server/common/web/static/img
mkdir -p server/common/web/static/js
mkdir -p server/common/web/templates/
cp client/build/index.html server/common/web/templates/
cp -r client/build/static server/common/web/
cp client/build/favicon.png server/common/web/static/img
cp client/build/service-worker.js server/common/web/static/js/


# TESTING
Expand Down Expand Up @@ -124,10 +124,6 @@ dev-env:
cd client && $(MAKE) ci
pip install -r server/requirements-dev.txt

.PHONY: gui-env
gui-env: dev-env
pip install -r server/requirements-gui.txt

# give PART=[major, minor, part] as param to make bump
.PHONY: bump
bump:
Expand Down Expand Up @@ -182,30 +178,3 @@ install-dist: uninstall
uninstall:
pip uninstall -y cellxgene || :


# GUI

.PHONY: build-assets
build-assets:
pyside2-rcc server/gui/cellxgene.qrc -o server/gui/cellxgene_rc.py

.PHONY: gui-spec-osx
gui-spec-osx: clean-lite gui-env
pip install -e .[gui]
pyi-makespec -D -w --additional-hooks-dir server/gui/ -n cellxgene --add-binary='/System/Library/Frameworks/Tk.framework/Tk':'tk' --add-binary='/System/Library/Frameworks/Tcl.framework/Tcl':'tcl' --add-data server/app/web/templates/:server/app/web/templates/ --add-data server/app/web/static/:server/app/web/static/ --icon server/gui/images/cxg_icons.icns server/gui/main.py
mv cellxgene.spec cellxgene-osx.spec

.PHONY: gui-spec-windows
gui-spec-windows: clean-lite dev-env
pip install -e .[gui]
pyi-makespec -D -w --additional-hooks-dir server/gui/ -n cellxgene --add-data server/app/web/templates;server/app/web/templates --add-data server/app/web/static;server/app/web/static --icon server/gui/images/icon.ico server/gui/main.py
mv cellxgene.spec cellxgene-windows.spec

.PHONY: gui-build-osx
gui-build-osx: clean-lite
pyinstaller --clean cellxgene-osx.spec

.PHONY: gui-build-windows
gui-build-windows: clean-lite
pyinstaller --clean cellxgene-windows.spec

41 changes: 0 additions & 41 deletions cellxgene-osx.spec

This file was deleted.

36 changes: 0 additions & 36 deletions cellxgene-windows.spec

This file was deleted.

12 changes: 0 additions & 12 deletions dev_docs/developer_scripts.md
Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,6 @@ Installs requirements files

```
dev-env - installs requirements and requirments-dev (for building code)
gui-env - installs requirements and requirments-dev and requirments-gui (for building native app)
```

### install commands
Expand All @@ -107,14 +106,3 @@ install-dist - installs from local dist folder
uninstall - uninstalls cellxgene
```

### gui

Commands for building the native app

```
build-assets - builds the image and icon assets for the gui to pull from
gui-spec-osx - creates the initial spec file for osx, do not run unless you are starting from scratch, one time only
gui-spec-windows - creates the initial spec file for windows, do not run unless you are starting from scratch, one time only
gui-build-osx - builds the app from the osx spec file
gui-build-windows - builds the app from the windows spec file
```
Binary file not shown.
Binary file not shown.
Binary file added example-dataset/pbmc3k.cxg/X/__array_schema.tdb
Binary file not shown.
File renamed without changes.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added example-dataset/pbmc3k.cxg/obs/__array_schema.tdb
Binary file not shown.
File renamed without changes.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added example-dataset/pbmc3k.cxg/var/__array_schema.tdb
Binary file not shown.
File renamed without changes.
Binary file not shown.
1 change: 0 additions & 1 deletion pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@ exclude = '''
| dist
| server/app/util/fbs/NetEncoding
)/
| server/gui/cellxgene_rc.py

)
'''
4 changes: 2 additions & 2 deletions server/Makefile
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
.PHONY: clean
clean:
rm -f app/web/templates/index.html
rm -rf app/web/static
rm -f common/web/templates/index.html
rm -rf common/web/static

.PHONY: unit-test
unit-test:
Expand Down