differences for PR #447

Author: actions-user

12-virtual-environments.md

@@ -483,67 +483,6 @@ six             1.16.0
 To uninstall a package installed in the virtual environment do: `python3 -m pip uninstall <package-name>`.
 You can also supply a list of packages to uninstall at the same time.
 
-### Installing Our Local Project as a Package Using `pip`
-
-Often when working on a Python project, the project itself will be a Python package (like `numpy` or `matplotlib` above) or at the very least it might be useful to treat it like a package.
-Said another way, it is usually the case we want a convenient way to call the Python code we are writing from another location, and making this code accessible as a package is the best way to do this.
-We will save the details of Python packaging for [a future episode](43-software-release.md), and for the meantime we can use the minimal package setup that our project already comes with, which is contained in the `pyproject.toml` file.
-Once again, we can use `pip` to install our local package:
-
-```bash
-python3 -m pip install --editable .
-```
-
-:::::::::::::::::::::::::::::::::::::::::  spoiler
-
-### This command fails for me
-
-If your `pip` installation is older than version 21.3, then this command will probably fail for you.
-This is because these older versions of `pip` do not support `pyproject.toml` as the package metadata.
-Given these versions of `pip` are now over 4 years old, we strongly recommend that you update `pip` if you can:
-
-```bash
-python3 -m pip install --upgrade pip
-```
-
-:::::::::::::::::::::::::::::::::::::::::
-
-This is similar syntax to above, with two important differences:
-
-1. The `--editable` or `-e` flag indicates that the package we are specifying should be an "editable" install.
-   An "editable" install is one that allows the package in our environment to change dynamically based on source code locally.
-   This is very convenient when we are developing the package because we can instantly see changes when we call the code from within our virtual environment, rather than having to install the local package again to get the updates.
-2. The argument `'.'` indicates that the package we want to install is located in the current directory.
-   The `pyproject.toml` file located in this directory then handles the rest.
-
-
-
-If we reissue the `pip list` command we should now see our local package with the name `python-intermediate-inflammation` in the output:
-
-```output
-Package                          Version     Editable project location
--------------------------------- ----------- ----------------------------------------------------------------------------------------------
-contourpy                        1.3.1
-cycler                           0.12.1
-exceptiongroup                   1.2.2
-fonttools                        4.56.0
-iniconfig                        2.0.0
-kiwisolver                       1.4.8
-matplotlib                       3.10.0
-numpy                            2.2.3
-packaging                        24.2
-pillow                           11.1.0
-pip                              22.0.2
-pluggy                           1.5.0
-pyparsing                        3.2.1
-pytest                           8.3.4
-python-dateutil                  2.9.0.post0
-python-intermediate-inflammation 0.0.0       /path/to/your/project/directory/python-intermediate-inflammation
-setuptools                       59.6.0
-six                              1.17.0
-tomli                            2.2.1
-```
-
 ### Exporting/Importing Virtual Environments Using `pip`
 
 You are collaborating on a project with a team so, naturally,
@@ -552,11 +491,12 @@ so they can easily 'clone' your software project with all of its dependencies
 and everyone can replicate equivalent virtual environments on their machines.
 `pip` has a handy way of exporting, saving and sharing virtual environments.
 
-To export your active environment use the `python3 -m pip freeze --exclude-editable` command to produce a list of packages installed in the virtual environment.
+To export your active environment -
+use `python3 -m pip freeze` command to produce a list of packages installed in the virtual environment.
 A common convention is to put this list in a `requirements.txt` file:
 
 ```bash
-(venv) $ python3 -m pip freeze --exclude-editable > requirements.txt
+(venv) $ python3 -m pip freeze > requirements.txt
 (venv) $ cat requirements.txt
 ```
 
@@ -578,7 +518,6 @@ The first of the above commands will create a `requirements.txt` file in your cu
 Yours may look a little different,
 depending on the version of the packages you have installed,
 as well as any differences in the packages that they themselves use.
-Also, we need to use the `--exclude-editable` command so that our local package is not included in the output, otherwise pip will try to pull from a specific commit at the time we made the editable install, which is not what we want.
 
 The `requirements.txt` file can then be committed to a version control system
 (we will see how to do this using Git in one of the following episodes)
@@ -587,10 +526,10 @@ They can then replicate your environment
 and install all the necessary packages from the project root as follows:
 
 ```bash
-(venv) $ python3 -m pip install -r requirements.txt --editable .
+(venv) $ python3 -m pip install -r requirements.txt
 ```
 
-As your project grows you may need to update your environment for a variety of reasons.
+As your project grows - you may need to update your environment for a variety of reasons.
 For example, one of your project's dependencies has just released a new version
 (dependency version number update),
 you need an additional package for data analysis (adding a new dependency)
@@ -665,7 +604,7 @@ to customize the command line.
 - Use `venv` to create and manage Python virtual environments.
 - Use `pip` to install and manage Python external (third-party) libraries.
 - `pip` allows you to declare all dependencies for a project in a separate file (by convention called `requirements.txt`) which can be shared with collaborators/users and used to replicate a virtual environment.
-- Use `python3 -m pip freeze --exclude-editable > requirements.txt` to take snapshot of your project's dependencies.
+- Use `python3 -m pip freeze > requirements.txt` to take snapshot of your project's dependencies.
 - Use `python3 -m pip install -r requirements.txt` to replicate someone else's virtual environment on your machine from the `requirements.txt` file.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::

13-ides.md

@@ -203,7 +203,7 @@ you may remember that we can get the list of packages in the current virtual env
 using `pip`:
 
 ```bash
-(venv) $ python3 -m pip list --exclude-editable
+(venv) $ python3 -m pip list
 ```
 
 ```output
@@ -231,7 +231,7 @@ if we want to see only the list of packages that we installed,
 we can use the `python3 -m pip freeze` command instead:
 
 ```bash
-(venv) $ python3 -m pip freeze --exclude-editable
+(venv) $ python3 -m pip freeze
 ```
 
 ```output
@@ -250,13 +250,13 @@ six==1.16.0
 
 We see the `pip` package in `python3 -m pip list` but not in `python3 -m pip freeze` 
 as we did not install it using `pip`.
-Remember that we use `python3 -m pip freeze --exclude-editable` to update our `requirements.txt` file,
+Remember that we use `python3 -m pip freeze` to update our `requirements.txt` file,
 to keep a list of the packages our virtual environment includes.
 Python will not do this automatically;
 we have to manually update the file when our requirements change using:
 
 ```bash
-python3 -m pip freeze --exclude-editable > requirements.txt
+python3 -m pip freeze > requirements.txt
 ```
 
 If we want, we can also see the list of packages directly in the following subdirectory of `venv`:
@@ -399,7 +399,7 @@ six==1.16.0
 `pytest` is missing from `requirements.txt`. To add it, we need to update the file by repeating the command:
 
 ```bash
-(venv) $ python3 -m pip freeze --exclude-editable > requirements.txt
+(venv) $ python3 -m pip freeze > requirements.txt
 ```
 
 `pytest` is now present in `requirements.txt`:

16-verifying-code-style-linters.md

@@ -44,7 +44,7 @@ $ python3 -m pip install pylint
 We should also update our `requirements.txt` with this new addition:
 
 ```bash
-$ python3 -m pip freeze --exclude-editable > requirements.txt
+$ python3 -m pip freeze > requirements.txt
 ```
 
 Pylint is a command-line tool that can help our code in many ways:

21-automatically-testing-software.md

@@ -614,7 +614,7 @@ Since we have installed `pytest` to our environment,
 we should also regenerate our `requirements.txt`:
 
 ```bash
-$ python3 -m pip freeze --exclude-editable > requirements.txt
+$ python3 -m pip freeze > requirements.txt
 ```
 
 Finally, let us commit our new `test_models.py` file,

22-scaling-up-unit-testing.md

@@ -213,7 +213,7 @@ Again, we should also update our `requirements.txt` file with our latest package
 which now also includes `pytest-cov`, and commit it:
 
 ```bash
-$ python3 -m pip freeze --exclude-editable > requirements.txt
+$ python3 -m pip freeze > requirements.txt
 $ cat requirements.txt
 ```
 

23-continuous-integration-automated-testing.md

@@ -128,10 +128,10 @@ Let us say we want to add more detail to our list of initial ascenders:
 ...
 first_scaled_by:
 - name: Hans Meyer
-  date_of_birth: 22-03-1858
+  date_of_birth: 1858-03-22
   nationality: German
 - name: Ludwig Purtscheller
-  date_of_birth: 22-03-1858
+  date_of_birth: 1858-03-22
   nationality: Austrian
 ```
 
@@ -200,7 +200,7 @@ jobs:
     - name: Install Python dependencies
       run: |
         python3 -m pip install --upgrade pip
-        python3 -m pip install -r requirements.txt .
+        python3 -m pip install -r requirements.txt
 
     - name: Test with PyTest
       run: |
@@ -244,7 +244,7 @@ Each of these steps are:
   In order to locally install our `inflammation` package
   it is good practice to upgrade the version of pip that is present first,
   then we use pip to install our package dependencies.
-  Notice that it is fine to omit the `--editable` flag in this case because the source code will be static and therefore we don't need this to be an "editable" install like when we are developing locally.
+  Once installed, we can use `python3 -m pip install -e .` as before to install our own package.
   We use `run` here to run theses commands in the CI shell environment
 - **Test with PyTest:** lastly, we run `python3 -m pytest`,
   with the same arguments we used manually before
@@ -383,10 +383,10 @@ jobs:
     - name: Install Python dependencies
       run: |
         python3 -m pip install --upgrade pip
-        python3 -m pip install -r requirements.txt .
+        python3 -m pip install -r requirements.txt
     - name: Test with PyTest
       run: |
-        python3 -m pytest --cov=inflammation.models tests/test_models.py
+        python3 -m pytest --cov=catchment.models tests/test_models.py
 ```
 
 The `{{ }}` are used

33-code-decoupling-abstractions.md

@@ -390,25 +390,17 @@ data sources with no extra work.
 
 Create another class that supports loading patient data from JSON files, with the
 appropriate `load_inflammation_data()` method.
-Here is an example function that you can add to your `models.py` file to load observations from a JSON file:
-```python
-def load_json(filename):
-    """Load a numpy array from a JSON document.
-    
-    Expected format:
-    [
-      {
-        "observations": [0, 1]
-      },
-      {
-        "observations": [0, 2]
-      }    
-    ]
-    :param filename: Filename of CSV to load
-    """
-    with open(filename, 'r', encoding='utf-8') as file:
-        data_as_json = json.load(file)
-        return [np.array(entry['observations']) for entry in data_as_json]
+There is a function in `models.py` that loads from JSON in the following format:
+
+```json
+[
+  {
+    "observations": [0, 1]
+  },
+  {
+    "observations": [0, 2]
+  }
+]
 ```
 
 Finally, at run-time, construct an appropriate data source instance based on the file extension.

41-code-review.md

@@ -321,14 +321,19 @@ There is doing to be an exercise next for you to practice it.
   repository as a collaborator.
   You will have to do the same for the collaborator doing the review on your repository.
 
-  **Note:** *You do not have to be a collaborator on a public repository to do code reviews
+  :::::::::::::::::::::::::::::::::::::::::  callout
+  
+  ## Code Review from External Contributors
+  
+  You do not have to be a collaborator on a public repository to do code reviews
   so this step is not strictly necessary.
   We are still asking you to do it now as we will get you working in teams
-  for the rest of the course so it may make sense to start setting up your collaborators now - as 
-  shown in the screenshot below.*
+  for the rest of the course so it may make sense to start setting up your collaborators now.
 
   ![](fig/github-add-collaborator.png){alt='Adding a collaborator in GitHub' .image-with-shadow width="900px"}
 
+  ::::::::::::::::::::::::::::::::::::::::::::::::::
+
 2. Locate up the pull request from the GitHub's `Pull Requests` tab on the home page
   of your fellow learner's software repository, then head to the `Files changed` tab
   on the pull request.

43-software-release.md

@@ -82,7 +82,7 @@ Poetry can also handle virtual environments for us,
 so in order to behave similarly to how we used them previously,
 let us change the Poetry config to put them in the same directory as our project:
 
-```bash
+```bash, bash
 $ poetry config virtualenvs.in-project true
 ```
 
@@ -111,17 +111,6 @@ although use your own contact details!*
 **NB: When you get to the questions about defining our dependencies,
 answer no, so we can do this separately later.**
 
-:::::::::::::::::::::::::::::::::::::::::  callout
-
-## It's Not Interactive?
-
-If you're using Git Bash for Windows, depending on your configuration, you may find after typing this command that you don't have an interactive set of questions displayed.
-Instead, you may find the `pyproject.toml` file is simply generated with a set of default values.
-
-If this happens, you can edit the `pyproject.toml` file and change the values in this file, similarly to how we have in the output below.
-
-:::::::::::::::::::::::::::::::::::::::::
-
 ```bash
 $ poetry init
 ```

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