Update TODO.md

- checked code with linters
- fixed some bugs 
- made package pip installable

TODO.md

@@ -5,18 +5,18 @@
 - [x] Formatting & cleanup of files
     * Remove unused imports (e.g. if package/function is imported but not used etc)
     * Maybe some reorganization and renaming of input files to make it more user-friendly (alpha_tools.py etc)?
-- [ ] Generate documentation (with `sphinx`)
+- [x] Generate documentation (with `sphinx`)
     * Quickstart guide on using `sphinx` [here](https://www.sphinx-doc.org/en/master/usage/quickstart.html)
     * The docs should include 3 main pages:
         1. Intro to what the package can do (index.rst)
         2. Python API for main functions (main_functions.rst)
         3. A good tutorial (as Jupyter Notebook) exemplifying the main functions & workflow
             * The notebook should combine `Markdown` and `Code` cells to explain the workflow, showing the outputs/plots etc
 - [ ] Publish docs in `Readthedocs`
-- [ ] Installation
-  - [ ] Enable `pip` install: this requires adding package to [pypi](https://pypi.org/)
+- [x] Installation
+  - [x] Enable `pip` install: this requires adding package to [pypi](https://pypi.org/)
 - [x] Update tutorial 1 to rewrite long code snippets as functions
-- [ ] Checking code & docstrings formatting with linters
+- [x] Checking code & docstrings formatting with linters
     * Using the packages `isort`, `black`, `pycodestyle`, `flake8`
 - [ ] Write up `JOSS` paper
   - Some examples here: