np: Review comments from gabriel.nuetzi

docs/review-comments.md

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+# Review Comments 💁
+
+## Project Structure 🚀
+
+The project is in good structure already. I like it!
+You did a good job. File-naming is consistent, nice small kebab-case folder names. Already in good shape with BPA Repository Guidelines I think, (also there is much more I like to see, later =)). Overall continue what I see and beeing clean and precise etc. ❤️
+
+All below items are equally important until prioritization:
+
+- `has_sample` variables in `.zarr` files implies `bool` values. Maybe consider
+  `sample(s)`. Check also for other use cases of this pattern.
+
+- Maybe add a `.modos` extension to `ZARR` root folder (representing the file
+  format). This gives the whole thing a much nicer semantic meaning. Yes its a file-format =).
+
+- Maybe put all top-level files `.bcf` etc. in `ZARR` files into `root/assets` (e.g. `root=<repo-root>/data/ex`). To make the toplevel of the file `.modos` clean. =)
+
+- I would introduce the following folder structure on top-level
+  to have it even more clean.
+
+  - move `modos` -> `src/modos` : The `modos` source code.
+  - move `data` -> `examples/`
+  - create `tools` : Tools and scripts needed in the future for this repository. Tooling around certain development aspects.
+  - move `deploy` -> `tools/deployment`: Move the folder maybe there.
+  - move `nix` -> `tools/nix`.
+
+  **or** if you want a more mono-repository structure:
+
+  - `components/modos`: the python component providing the python source code, its a folder which acts as a full python project.
+
+  - `components/modos-backend` : the stuff which is needed to deploy the `backend`, e.g. `htsget` etc...
+
+  This mono-repo structure makes it easier to add more stuff later, if we need another micro-service or a database etc.
+  But maybe overkill for now!
+
+- Provide a `.devcontainer` such that `code` users can simply run everything inside this container. I can make a short PR on this providing the minimal setup (ubuntu with nix installed, nice shell, etc). To make it more proper:
+  _We need a `python` dev-container maintained centrally to pull this off properly. I can provide all this but needs discussion first in BPA and SDSC in general how you did things etc._
+
+- Maybe do not write `.bat` files (reasons on 1-to-1 😃), maybe `make.bat` was autogenerated or so. But Windows users are much encouraged to use `git-bash.exe` (`bash.exe`) and everything in this repository should work out of the box. Or they should use the `.devcontainer` with `code`. This should be maybe \*nix only.
+
+- Write all titles in markdown files capitalized (correct English). I am somewhat unsure with stuff like `Welcome to the modos-api documentation`.
+  But I think consistency matters more. (?)
+
+- Change `Makefile` to `justfile`: Its a better and nicer command runner. `make` is really old and has some arcane workings I want nobody to expose to =).
+
+## Code Review 🐊
+
+TODO: ...