misc linting

.gitignore

@@ -1,12 +1,10 @@
-.vscode
-
-cpp/generated/
-cpp/build/
-
-python/petsird/
-**/__pycache__/
+/cpp/generated/
+/cpp/build/
+/python/petsird/
+__pycache__/
 
 # Common editor backups
+/.vscode/
 ~$*
 *~
 *.bak

README.md

@@ -3,6 +3,7 @@
 The purpose of this repo is to have a simple working example of a data model for PET imaging (list mode data). This is **not complete**, and aspects do not follow the actual proposal of PETSIRD yet.
 
 ## Background
+
 The [Emission Tomography Standardization Initiative (ETSI)](https://etsinitiative.org/)
 is working towards establishing a standard for PET Raw Data, called PETSIRD ("PET ETSI Raw Data").
 
@@ -17,9 +18,11 @@ in a [VS Code devcontainer](https://code.visualstudio.com/docs/devcontainers/con
 This codespace/container will contain all necessary tools, including `yardl` itself, as well as the current repository.
 2. Browse the [`model`](./model/README.md) directory.
 3. Use `yardl` to generate C++ and Python code for the model:
-  ```sh
-  cd model
-  yardl generate
-  ```
+
+   ```sh
+   cd model
+   yardl generate
+   ```
+
 4. Have a look at (and try!) the examples in the [`cpp`](cpp/README.md) and/or
 [`python`](python/README.md) directories.

cpp/README.md

@@ -5,15 +5,15 @@ This directory contains some C++ example code to read/write PETSIRD data. You ne
 The C++ code shows writing to and reading from an HDF5 file
 
 1. Compile the code:
+
    ```sh
-   cd /whereever/cpp
-   mkdir -p build && cd build`
-   cmake -G Ninja -S .. -DHDF5_ROOT=$CONDA_PREFIX
-   ninja`
+   mkdir -p build
+   cmake -G Ninja -S . -B build -DHDF5_ROOT=$CONDA_PREFIX
+   ninja
    ```
+
    If you did not use `conda` to install HDF5, do not add the `-DHDF5_ROOT=$CONDA_PREFIX` part of the `cmake` line.
 
 2. Run the generator: `./petsird_generator test.h5`
 3. Run the analyzer: `./petsird_analysis test.h5`
 4. You can inspect the HDF5 file by running `h5dump test.h5`
-

python/README.md

@@ -9,7 +9,8 @@ reading it from standard in. This can be used as follows:
 1. `python petsird_generator.py | python petsird_analysis.py`
 
 There is also a very basic utility to plot the scanner geometry. For instance
-```
-python petsird_generator.py > test.bin
-python petsird_plot_scanner.py < test.bin`
 
+```sh
+python petsird_generator.py > test.bin
+python petsird_plot_scanner.py < test.bin
+```