Skip to content

Commit

Permalink
Nose to pytest
Browse files Browse the repository at this point in the history
  • Loading branch information
@asistradition
asistradition committed Jun 9, 2022
1 parent 8638d2f commit cdeb427
Showing 1 changed file with 64 additions and 35 deletions.
99 changes: 64 additions & 35 deletions devnotes.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,25 +41,34 @@ and click "fork"

## Install the necessary packages (once)

In order to work with the forked repository you will need `git` and a number of
other tools.
In order to work with the forked repository you will need `git`.

```
sudo apt-get install python-dev
sudo apt-get install python-pip
sudo apt-get install python-nose
sudo apt-get install git
python -m pip install numpy
python -m pip install pandas
```

Download and install [miniconda](https://docs.conda.io/en/latest/miniconda.html).
Create a new conda environment for the inferelator.

```
conda create --name inferelator python=3.10
```

Switch to the inferelator environment and install the required dependencies

```
conda activate inferelator
python -m pip install numpy scipy sklearn pandas joblib anndata matplotlib
```


## Configuring your `git` command line interface

You might want to follow these instructions in case your name and email are not set properly (you should only need to do this once):

```
git config --global user.name "Your Name"
git config --global user.email [email protected]
git config --global user.name "Your Name"
git config --global user.email [email protected]
```
This allows git to associate your name and email with any changes you make.

Expand All @@ -74,6 +83,12 @@ To clone the fork onto your workstation type in the terminal:
git clone $URL
```

Create package links in the inferelator environment to finish installation:

```
python setup.py develop
```

## Set up the "remote" repository (once)

You will want to periodically
Expand Down Expand Up @@ -109,36 +124,50 @@ Unit tests attempt to check that everything is working properly.
It is a good idea to run unit tests frequently, especially before making
changes and after making changes but before committing them.

Run unit tests from the shell with the [nosetests](http://pythontesting.net/framework/nose/nose-introduction/) command
Run unit tests from the shell with the [pytest](https://docs.pytest.org/) command
(this runs the unit tests):

```bash
python -m nose
python -m pytest
```

Output should look like this:

```
...........................................SS.........................
......................................................................
......................................................................
........................
----------------------------------------------------------------------
Ran 241 tests in 14.257s
OK (SKIP=2)
```

Each dot stands for a unit test that ran, "S" stands for "Skipped". If there are
=================================== test session starts ====================================
platform linux -- Python 3.8.3, pytest-7.1.2, pluggy-0.13.1
rootdir: /home/chris/PycharmProjects/inferelator
collected 347 items
inferelator/tests/test_amusr.py .......... [ 2%]
inferelator/tests/test_base_regression.py .... [ 4%]
inferelator/tests/test_bayes_stats.py .................... [ 9%]
inferelator/tests/test_bbsr.py ........... [ 12%]
inferelator/tests/test_crossvalidation_wrapper.py ....................... [ 19%]
inferelator/tests/test_data_loader.py ....... [ 21%]
inferelator/tests/test_data_wrapper.py ...................................... [ 32%]
inferelator/tests/test_design_response.py ............ss.. [ 37%]
inferelator/tests/test_elasticnet_python.py .... [ 38%]
inferelator/tests/test_mi.py ............... [ 42%]
inferelator/tests/test_mpcontrol.py ................. [ 47%]
inferelator/tests/test_noising_data.py .......... [ 50%]
inferelator/tests/test_priors.py .............. [ 54%]
inferelator/tests/test_regression.py .................... [ 60%]
inferelator/tests/test_results_processor.py ........................................ [ 71%]
.ss.... [ 73%]
inferelator/tests/test_single_cell.py ......... [ 76%]
inferelator/tests/test_tfa.py ......... [ 78%]
inferelator/tests/test_utils.py ............. [ 82%]
inferelator/tests/test_workflow_base.py ..................................... [ 93%]
inferelator/tests/test_workflow_multitask.py ............... [ 97%]
inferelator/tests/test_workflow_tfa.py ........ [100%]
====================== 343 passed, 4 skipped, 224 warnings in 35.34s =======================
```

Each dot stands for a unit test that ran, "s" stands for "Skipped". If there are
failures the output will be more extensive, describing which tests failed and how.

For debugging purposes it is sometimes useful to use `print` statements and invoke
nosetests with the `--nocapture` option in order to see the output.

```bash
python -m nose --nocapture
```

# Making a contribution to the project

Before you make a change you want to contribute to the project it
Expand All @@ -155,28 +184,28 @@ To test the process you can go try the following:
cd inferelator/
```

Change one of the files (for example the `utils.py` file), by adding a blank line or something.
Change one of the files (for example the `workflow.py` file), by adding a blank line or something.

## Run Unit Tests again to make sure everything still works

run nosetests (this runs the unit tests):
run pytest (this runs the unit tests):

```
python -m nose
python -m pytest
```

## Push your changes to your Github directory

For each file you altered, run the following command:

```
git add utils.py
git add workflow.py
```

After you've done this for every file you've changed (in this case it's just 1 file), commit the changes to your fork by running:

```
git commit -m "fixed utils.py"
git commit -m "fixed workflow.py"
```
It is a good idea to commit the files you intended to change one at a time
to make sure you don't add unintended changes to the commit.
Expand All @@ -196,7 +225,7 @@ Someone with write access to the master repository will look over your changes.
approve, or close your request.

An approver may ask for changes before approving your pull request. You can add changes by pushing
more commits (to the same branch of your forked repository, in this case the `master` branch).
more commits (to the same branch of your forked repository, in this case the `release` branch).

## More sophisticated work flows

Expand Down

0 comments on commit cdeb427

Please sign in to comment.