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| author | Muriithi Frederick Muriuki | 2021-08-08 11:06:35 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-08 11:06:35 +0300 |
| commit | 0ec39e6c5058f4f06bfb5f763f51cd9dc176cb35 (patch) | |
| tree | 2c9ea26f67e2a451343f4003fb67478baeb17ec2 /README.md | |
| parent | a73d1ce388012758ce3b0d789f008e4184e6a38e (diff) | |
| parent | e0476d51603432f60b6412b65486166deabe9e08 (diff) | |
| download | genenetwork3-0ec39e6c5058f4f06bfb5f763f51cd9dc176cb35.tar.gz | |
Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_decompose_db_retrieval
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 41 |
1 files changed, 37 insertions, 4 deletions
diff --git a/README.md b/README.md index c1acba1..c3a9848 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ Simply load up the environment (for development purposes): guix environment --load=guix.scm ``` -Also, make sure you have the *guix-bioinformatics* channel set up. +Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up. ```bash env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --load=guix.scm @@ -22,9 +22,21 @@ python3 Better run a proper container ``` -env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm +env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm ``` +If you get a Guix error, such as `ice-9/boot-9.scm:1669:16: In procedure raise-exception: +error: python-sqlalchemy-stubs: unbound variable` it typically means an update to guix latest is required (i.e., guix pull): + +``` +guix pull +source ~/.config/guix/current/etc/profile +``` + +and try again. + +See also instructions in [.guix.scm](.guix.scm). + #### Running Tests (assuming you are in a guix container; otherwise use venv!) @@ -49,12 +61,33 @@ mypy . #### Running the flask app -To spin up the server: +To spin up the server on its own (for development): ```bash env FLASK_DEBUG=1 FLASK_APP="main.py" flask run --port=8080 ``` +And test with + +``` +curl localhost:8080/api/version +"1.0" +``` + +To run with gunicorn + +``` +gunicorn --bind 0.0.0.0:8080 wsgi:app +``` + +consider the following options for development `--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload wsgi`. + +And for the scalable production version run + +``` +gunicorn --bind 0.0.0.0:8080 --workers 8 --keep-alive 6000 --max-requests 10 --max-requests-jitter 5 --timeout 1200 wsgi:app +``` + ##### Using python-pip IMPORTANT NOTE: we do not recommend using pip tools, use Guix instead @@ -71,7 +104,7 @@ virtualenv --python python3 venv ```bash # The --ignore-installed flag forces packages to -# get installed in the venv even if they existed +# get installed in the venv even if they existed # in the global env pip install -r requirements.txt --ignore-installed ``` |