address some feedback from oct-2023

.github/workflows/update-issue.yaml

@@ -7,13 +7,17 @@ on:
 jobs:
   create_issues:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      issues: write
     steps:
     - name: Checkout repository
       uses: actions/checkout@v2
 
     - name: Create issues from markdown files
       run: |
-        for file in .issues/*.md; do
+        cd .issues/
+        for file in $( ls | sort -n ); do
           title=$(head -n 1 $file)
           body=$(tail -n +2 $file)
           echo "Creating issue with title: $title"

.issues/exercise_1.md

@@ -2,13 +2,13 @@
 
 ## Setup your playground
 
-Please follow these instructions step-by-step before the course starts.
+Please follow these instructions step-by-step.
 
-### 1. Fork this repository
+### Fork this repository
 
 ![Indicates where the Fork button is (top-right corner of the repository page)](https://i.imgur.com/HiBlmrj.png)
 
-### 2. Clone your repository locally
+### Clone your repository locally
 
 In a `bash` terminal on your computer, run:
 ```bash
@@ -23,10 +23,21 @@ A folder named `rse-best-practices-playground` should be listed.
 
 (If this does not work, you may have to set up a personal access token: Follow the instructions [in the GitHub documentation](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-fine-grained-personal-access-token) and get in touch with the course organisers if you encounter issues.)
 
-### 3. React to this issue with :+1:
+### Create a conda environment for your playground
+
+In your command line, run
+
+```{.bash}
+conda create -n "software-good-practice-course" python=3.11 
+```
+```{.bash}
+conda activate software-good-practice-course
+```
+
+### React to this issue with :+1:
 ![Select and add a reaction to this comment](https://user-images.githubusercontent.com/963242/95435873-0bcb4480-094b-11eb-9d37-2fdefdcb8c6f.png)
 
 The next exercises will be described in the issues of the original repository (the one you made your fork from).
-### 4. (Optional) Have a look at the code
+### (Optional) Have a look at the code
 
 You may want to study the code in `times.py`. You can find it by navigating to `rse-best-practices-playground` > `rse_best_practices_playground` > `times.py`. Can you figure out what the code is meant to do?

.issues/exercise_2.md

@@ -3,20 +3,25 @@ This exercise will show how to do write a docstring.
 
 ## Setup
 We suggest using [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html), i.e. the Numpy style guide for docstrings.
+Checkout a new branch named `add-docstring` using `git`.
+
+```bash
+git checkout -b add-docstring
+```
 
 ## Write a docstring
 The method `calculate_fastest_time` in `times.py` doesn't have a docstring. Based on your understanding of the method, write a docstring using Numpy formatting. Describe what the method does, what are the inputs and the outputs.
 
 ## Submit a Pull Request
 Once you have completed or made progress on the exercise, commit your changes, push them to your fork and open a pull request and ask for a review.
 
-Create a **pull request (PR)** from your branch to `rse-best-practices-course-2023/rse-best-practices-playground` [using the GitHub web interface](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request).
+Create a **pull request (PR)** from your branch to `UCL-bioimage-analysis/rse-best-practices-playground` [using the GitHub web interface](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request).
 
-Add a meaningful title to that PR and a link to this issue: `rse-best-practices-course-2023/rse-best-practices-playground#2`.
+Add a meaningful title to that PR and a link to this issue: `UCL-bioimage-analysis/rse-best-practices-playground-2024#2`.
 
 ## [Optional 1] Review a Pull Request
 If you already completed the above exercise, you can review a PR from another participant. You can find the submitted PRs in the [GitHub interface](
-    https://www.github.com/rse-best-practices-course-2023/rse-best-practices-playground/pulls).
+    https://www.github.com/UCL-bioimage-analysis/rse-best-practices-playground/pulls).
 
 ## [Optional 2] Write docstrings for other methods
 If you have time, write docstrings for the other methods in `times.py` and submit a new PR.

.issues/exercise_3.md

@@ -1,5 +1,5 @@
 # Exercise 3
-This exercise will look at write a test to check that it works as expected.
+This exercise will look at write a test to check that our function works as expected.
 
 ## Setup
  Install the playground as a developer (`".[dev]"`), in editable (`-e`) mode, by navigating into the `rse-best-practices-playground` folder and running
@@ -8,6 +8,12 @@ pip install -e ".[dev]"
 ```
 In this way you will have installed `pytest` and other useful tools for development.
 
+Checkout a new branch named `add-test` using `git`.
+
+```bash
+git checkout -b add-test
+```
+
 ## Write a test
 The next step consists of converting the __main__ part of the code into a unit test.
     i. Create a new file called `test_times.py` in the same directory where `times.py` is.
@@ -27,9 +33,9 @@ Run `pytest` on that directory and see whether the test is picked up by `pytest`
 ## Submit a Pull Request
 Once you have completed or made progress on the exercise, commit your changes, push them to your fork and open a pull request and ask for a review.
 
-Create a **pull request (PR)** from your branch to `rse-best-practices-course-2023/rse-best-practices-playground` [using the GitHub web interface](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request).
+Create a **pull request (PR)** from your branch to `UCL-bioimage-analysis/rse-best-practices-playground-2024` [using the GitHub web interface](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request).
 
-Add a meaningful title to that PR and a link to this issue: `rse-best-practices-course-2023/rse-best-practices-playground#3`.
+Add a meaningful title to that PR and a link to this issue: `UCL-bioimage-analysis/rse-best-practices-playground-2024#3`.
 
 ## [Optional 1] Write more tests for `calculate_fastest_time`
 Do you see any other ways the method `calculate_fastest_time` could fail?

.issues/exercise_4.md

@@ -5,21 +5,29 @@ For this exercise, we will look at how to rewrite (refactor) existing code in di
 According to what was presented in the slides, do you see ways to reduce duplication?
 Focus on the method `print_fastest_time` in `times.py`.
 
+## Setup
+
+Checkout a new branch named `refactor` using `git`.
+
+```bash
+git checkout -b refactor
+```
+
 ## Review your changes
 Run your script. Does it still behave as expected?
 **Do your tests still pass?**
 
 ## Submit a Pull Request
 Once you have completed or made progress on the exercise, commit your changes, push them to your fork and open a pull request and ask for a review.
 
-Create a **pull request (PR)** from your branch to `rse-best-practices-course-2023/rse-best-practices-playground` [using the GitHub web interface](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request).
+Create a **pull request (PR)** from your branch to `UCL-bioimage-analysis/rse-best-practices-playground-2024` [using the GitHub web interface](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request).
 
 Add a meaningful title to that PR and a link to this issue: `rse-best-practices-course-2023/rse-best-practices-playground#4`.
 
 
 ## [Optional 1] Review a Pull Request
 If you already completed the above exercise, you can review a PR from another participant. You can find the submitted PRs in the [GitHub interface](
-    https://www.github.com/rse-best-practices-course-2023/rse-best-practices-playground/pulls).
+    https://www.github.com/UCL-bioimage-analysis/rse-best-practices-playground-2024/pulls).
 
 ## [Optional 2] Refactor other methods
 If you have time, refactor the other methods in `times.py` and submit a new PR.