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authorAlexander Kabui2021-05-15 01:20:46 +0300
committerGitHub2021-05-15 01:20:46 +0300
commitc69b11cffba7547d65ac9812b0118cddad91be0d (patch)
treebfa55c23f702db5072e8839e44961dd72fd4a9e2 /README.md
parentbcba700bd2835f0a36042d781860b3407519f6d8 (diff)
parent46a96ec0b89620eed4874ada565a9643ac19a042 (diff)
downloadgenenetwork3-c69b11cffba7547d65ac9812b0118cddad91be0d.tar.gz
Merge branch 'main' into feature/minor-fixes
Diffstat (limited to 'README.md')
-rw-r--r--README.md49
1 files changed, 31 insertions, 18 deletions
diff --git a/README.md b/README.md
index b18fdf1..c1acba1 100644
--- a/README.md
+++ b/README.md
@@ -3,34 +3,27 @@ GeneNetwork3 REST API for data science and machine learning
## Installation
-##### Using python-pip
+#### Using guix
-1. Prepare your system. You need to make you have python > 3.8, and
- the ability to install modules.
-2. Create and enter your virtualenv:
+Simply load up the environment (for development purposes):
```bash
-virtualenv --python python3 venv
-. venv/bin/activate
+guix environment --load=guix.scm
```
-3. Install the required packages
+
+Also, make sure you have the *guix-bioinformatics* channel set up.
```bash
-# The --ignore-installed flag forces packages to
-# get installed in the venv even if they existed
-# in the global env
-pip install -r requirements.txt --ignore-installed
+env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --load=guix.scm
+python3
+ import redis
```
-#### Using guix
+Better run a proper container
-Simply load up the environment (for development purposes):
-
-```bash
-guix environment --load=guix.scm
```
-
-Also, make sure you have the *guix-bioinformatics* channel set up.
+env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm
+```
#### Running Tests
@@ -62,6 +55,26 @@ To spin up the server:
env FLASK_DEBUG=1 FLASK_APP="main.py" flask run --port=8080
```
+##### Using python-pip
+
+IMPORTANT NOTE: we do not recommend using pip tools, use Guix instead
+
+1. Prepare your system. You need to make you have python > 3.8, and
+ the ability to install modules.
+2. Create and enter your virtualenv:
+
+```bash
+virtualenv --python python3 venv
+. venv/bin/activate
+```
+3. Install the required packages
+
+```bash
+# The --ignore-installed flag forces packages to
+# get installed in the venv even if they existed
+# in the global env
+pip install -r requirements.txt --ignore-installed
+```
#### A note on dependencies