Another attempt

.github/workflows/generate_readme.yaml

@@ -19,17 +19,19 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install (without dependencies)
+      python -m pip install . --no-deps
     - name: Get argparse help outputs
       run: |
-        cd src/sim_recon/cli
-        export OTF_HELP_OUTPUT=$(python -c "import parsing; parsing.parse_otf_args(("--help",))")
-        export RECON_HELP_OUTPUT=$(python -c "import parsing; parsing.parse_recon_args(("--help",))")
+        export OTF_HELP_OUTPUT=$(python -c "from sim_recon.cli.parsing import parse_otf_args; parse_otf_args(("--help",))")
+        export RECON_HELP_OUTPUT=$(python -c "from sim_recon.cli.parsing import parse_recon_args; parse_recon_args(("--help",))")
     - name: Get sections
       run: |
-        cd docs
+        cd docs/
         for file in sections/*; do 
             if [ -f "$file" ]; then 
-              var_name="$(echo "${file^^}" | tr "./" "_")"
+              var_name="$(echo "${file^^}" | tr ./ _)"
+              echo "Saving $file to $var_name"
               # Export file contents to an environment variable named from the path, e.g.:
               # 'section/test_file.md' would be 'SECTION_TEST_FILE_MD'
               export "${!var_name}"="$(<"$file")"