17 pop merge resample (#30)

* chore: added dev work from experiment/pop-exploration

* feat: added skeleton merge and resample functions

* feat: raster merge input file handling

* feat: working raster merge func

* feat: sorted tif files list to simplify QA

* feat: added merge unit test dev

* feat: added merge raster unit test

* feat: working resample function

* docs: added raises to  merge function docstring

* fix: correct fixture scope

* test: added raster resampling test

* fix: added geos install for catopy

* docs: added comment to geos install

* chore: deleted utils placeholder.py

* docs: added dependencies section; restructured set-up section

* chore: added seaborn to

* docs: corrected typo

* feat: added defense on missing tif post regex

* chore: reset area of interest

* feat: added dir creation if not already exists

* feat: added references to 2015 data sources

.github/workflows/python-package.yml

@@ -23,6 +23,11 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install geos  # required for cartopy installation
+      uses: ConorMacBride/install-package@v1
+      with:
+        brew: geos
+        apt: libgeos-dev
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

CONTRIBUTING.md

@@ -16,12 +16,20 @@ Please read [`CODE_OF_CONDUCT.md`](CODE_OF_CONDUCT.md) before contributing.
 
 ### Set-up
 
-| Set-up expectations | |
+Set-up expectations:
+
+|  | |
 | --- | --- |
 | Env manager: | conda |
 | Os: | macOS |
 | Package manager: | pip |
 
+Install Dependencies:
+
+0. There are a few dependencies that need to be installed in advance. See the [dependencies section](#markdown-header-dependencies) for specific instructions and then return here once they have been installed.
+
+Package set-up and installation:
+
 1. Setup a new conda env: `conda create -n r5py python=3.9.13`
 2. Activate the environment: `conda activate r5py`
 3. Launch terminal and change directory to wherever you keep your GitHub repos: `cd ~/Documents`
@@ -31,25 +39,35 @@ Please read [`CODE_OF_CONDUCT.md`](CODE_OF_CONDUCT.md) before contributing.
 7. Update pip: `pip install --upgrade pip`
 8. Install r5py & other reqs: `pip install -r requirements.txt`
 
-**Java Development Kit**
-Openjdk 11 is recommended by r5py docs. [sdkman](https://sdkman.io/) is used here.
+Set-up check:
 
-9. Get sdkman: `curl -s "https://get.sdkman.io" | bash`
-10. Follow instructions in terminal, you’ll be asked to: `source “<SOME_PATH>.sdkman/bin/sdkman-init.sh"`
-This will add sdkman env variables to: `~/.bash_profile` and possibly `~/.zshrc` too.
-11. To see versions available on your os: `sdk list java`
-12. Install the required version using the `identifier` column, eg: `sdk install java 11.0.19-amzn`
-13. Check this is the currenty used java version: `sdk current java`
+10. Run set-up pytests: `pytest --runsetup`.
+11. If everything is working as expected, you should see some Java flavoured warnings about `--illegal-access` that you can ignore. But importantly look out for the message: `r5py has created the expected database files.`
+12. If you've made it this far, you've earned yourself a coffee.
 
-> Note: for macOS on ARM architectures (M1/M2 machines), sdkman does not currently provide a suitable openjdk11 version. Instead you can follow this [blog post, which introduces Java version mangaement using `jEnv`](https://blog.bigoodyssey.com/how-to-manage-multiple-java-version-in-macos-e5421345f6d0), and install AdoptOpenJDK-11. You can then continue with the remainder of the steps below.
+#### Dependencies
 
-**Set-up check**
+##### Geos
 
-14. Now you should be able to run the check setup script, from terminal: `python3 src/utils/check-setup.py`
-15. If everything is working as expected, you should see some Java flavoured warnings about `--illegal-access` that you can ignore. But importantly look out for the message: `r5py has created the expected database files.`
-16. Run set-up pytests: `pytest --runsetup`.
-17. If you've made it this far, you've earned yourself a coffee.
+`geos` is a dependency of the python package `cartopy`, which is used here for building and visualising static maps. See [this cartopy installation guidance note](https://github.com/SciTools/cartopy/blob/main/INSTALL) for more details on the installation process.
 
+For macOS, this is straight forward using `brew`:
+
+```console
+brew install geos
+```
+
+##### Java Development Kit
+Java is required for handling the transport network routing. Openjdk 11 is recommended by r5py docs. [sdkman](https://sdkman.io/) is used here.
+
+> Note: for macOS on ARM architectures (M1/M2 machines), sdkman does not currently provide a suitable openjdk11 version. Instead you can follow this [blog post, which introduces Java version mangaement using `jEnv`](https://blog.bigoodyssey.com/how-to-manage-multiple-java-version-in-macos-e5421345f6d0), and install AdoptOpenJDK-11.
+
+1. Get sdkman: `curl -s "https://get.sdkman.io" | bash`
+2. Follow instructions in terminal, you’ll be asked to: `source “<SOME_PATH>.sdkman/bin/sdkman-init.sh"`
+This will add sdkman env variables to: `~/.bash_profile` and possibly `~/.zshrc` too.
+3. To see versions available on your os: `sdk list java`
+4. Install the required version using the `identifier` column, eg: `sdk install java 11.0.19-amzn`
+5. Check this is the currenty used java version: `sdk current java`.
 
 ### Pre-commit