Try to build README from sections and code

.github/workflows/argparse_help_to_readme.yaml

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+name: Pylint
+
+on:
+  pull_request:
+    paths:
+      - "docs/*.md"
+      - "src/sim_recon/cli/parsing.py"
+      - "src/sim_recon/settings/formatting.py"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Get argparse help outputs
+      run: |
+        cd src/sim_recon/cli
+        export OTF_HELP_OUTPUT=$(python -c "import parsing; parsing.parse_otf_args(("--help",))")
+        export RECON_HELP_OUTPUT=$(python -c "import parsing; parsing.parse_recon_args(("--help",))")
+    - name: Get sections
+      run: |
+        cd docs/sections
+        for file in *; do 
+            if [ -f "$file" ]; then 
+              var_name=${file^^}_SECTION
+              # Export file contents to <FILENAME>_SECTION
+              export "${!var_name}"= <"$file"
+              envsubst < "${!var_name}"
+            fi 
+        done
+    - name: Fill template
+      run: |
+        cp -f docs/template.md README.md
+        envsubst < README.md

docs/sections/command_line.md

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+### CLI
+
+##### sim-otf
+```
+${{ env.OTF_HELP_OUTPUT }}
+```
+
+
+##### sim-recon
+```
+${{ env.RECON_HELP_OUTPUT }}
+```
+
+##### dv2tiff
+Accepts a list of DV files to be converted to TIFFs (with some OME metadata).
+
+##### otf-view
+Accepts a list of OTF files (DV or TIFF), the amplitude and phase of which will be plotted.

docs/sections/configuration.md

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+### Configuration
+Calls to `sim-otf` and `sim-recon` can both take a `-c`/`--config` argument. This should be similar to the `config.ini` file in the configs directory, which specifies the defaults config, any per-channel configs (some values should be set on a per-channel basis), and the locations of OTFs for each channel.
+The channels are specified based on the emission wavelength in nanometres (must be an integer).
+##### Example:
+For a channel with an emission wavelength of 525nm:
+- In the `[configs]` section, the channel config can be specified as `525=/path/to/configs/525.cfg`
+- In the `[otfs]` section, the channel OTF file can be specified as `525=/path/to/otfs/525_otf.tiff`
+A directory can be specified within each of the `[configs]` and `[otfs]` sections. If given, files can also be defined relative to that directory, e.g. if `directory=/path/to`, then `525=/path/to/otfs/525_otf.tiff` could simply be `525=otfs/525_otf.tiff`.
+Config settings will be overriden by higher-priority sources.
+
+##### Order of setting priority:
+1. Command line arguments (override all)
+2. Per-channel configs (override defaults for the appropriate channel only)
+3. Defaults (override any cudasirecon defaults)

docs/template.md

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+# PySIMRecon
+
+Easy to use wrapper for pyCUDAsirecon, allowing the use of DV (DeltaVision) files without IVE/Priism (UCSF library with MRC/DV support).
+
+This is built for easy use from the command line or as part of an auto-processing pipeline, allowing parameters to be pre-configured or defined at runtime.
+
+### Goal
+
+To reconstruct the SIM data and create OTFs from PSFs from the cryoSIM at B24, Diamond from the .dv files created by Cockpit. Requirements are:
+
+- Easy to use
+- Open source
+- Reproducable results
+- Can be used as part of an automatic processing pipeline
+
+### Current state
+
+Under development
+
+${{ env.CONFIGURATION_SECTION }}
+
+${{ env.COMMAND_LINE_SECTION }}