Skip to content

Commit

Permalink
add info about loose and stable install to the readme
Browse files Browse the repository at this point in the history
  • Loading branch information
ammarcsj committed Jul 19, 2024
1 parent 936da01 commit e180557
Showing 1 changed file with 9 additions and 2 deletions.
11 changes: 9 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -37,14 +37,19 @@ The GUI of AlphaMap is a completely stand-alone tool that requires no knowledge

AlphaMap can be installed in an existing Python 3.8 environment with a single `bash` command. *This `bash` command can also be run directly from within a Jupyter notebook by prepending it with a `!`*.

```bash
pip install alphamap[stable]
```
The [stable] tag ensures you get the latest stable release with fixed dependencies. However, it can be omitted if you prefer more flexible dependency versions:

```bash
pip install alphamap
```

When a new version of AlphaMap becomes available, the old version can easily be upgraded by running e.g. the command again with an additional `--upgrade` flag:

```bash
pip install alphamap --upgrade
pip install --upgrade alphamap[stable]
```

NOTE: When installing with `pip`, UniProt information is not included. Upon first usage of a specific Organism, its information will be automatically downloaded from UniProt.
Expand All @@ -71,11 +76,13 @@ For any Python package, it is highly recommended to use a [conda virtual environ
```bash
conda create -n alphamap python=3.8 -y
conda activate alphamap
pip install -e .
pip install -e ".[stable]"
```

* By using the editable flag `-e`, all modifications to the AlphaMap [source code folder](alphamap) are directly reflected when running AlphaMap. Note that the AlphaMap folder cannot be moved and/or renamed if an editable version is installed.

* The [stable] tag ensures you get the latest stable release with fixed dependencies. However, it can be omitted if you prefer more flexible dependency versions.

* When using Jupyter notebooks and multiple conda environments direcly from the terminal, it is recommended to `conda install nb_conda_kernels` in the conda base environment. Hereafter, running a `jupyter notebook` from the conda base environment should have a `python [conda env: alphamap]` kernel available, in addition to all other conda kernels in which the command `conda install ipykernel` was run.


Expand Down

0 comments on commit e180557

Please sign in to comment.