Fix and update example readme, add openmm.org/development to URL check excludes

.github/workflows/CI.yml

@@ -634,19 +634,19 @@ jobs:
         shell: bash -l {0}
         env:
           # Pipe-seperated list of domains to skip
-          SKIP_DOMAIN: support.amd.com|www.pnas.org|doi.org|commonfund.nih.gov
+          SKIP_DOMAIN: support.amd.com|www.pnas.org|doi.org|commonfund.nih.gov|openmm.org/development
         run: |
           set +e
           # Linkinator accepts regex for its --skip argument, so we
           # should pre-process the domains into the relevant pattern
           SKIP_REGEX=$(python -c "print(
-            '^(https?://)?([a-zA-Z0-9\-_.]+\.)?', # Optionally match protocol and subdomains
-            '(',                                  # Open sub-pattern for domain names
-              '$SKIP_DOMAIN'.replace('.', '\.'),     # Escape out periods
-            ')',                                  # Close sub-pattern of domains
-            '(/.*)?$',                            # only match if this is the end of the domain name
-            sep='',                               # Concatenate the above strings exactly
-            end=''                                # No newline at end of print()
+            r'^(https?://)?([a-zA-Z0-9\-_.]+\.)?', # Optionally match protocol and subdomains
+            '(',                                   # Open sub-pattern for domain names
+              '$SKIP_DOMAIN'.replace('.', r'\.'),  # Escape out periods
+            ')',                                   # Close sub-pattern of domains
+            '(/.*)?$',                             # only match if this is the end of the domain name
+            sep='',                                # Concatenate the above strings exactly
+            end=''                                 # No newline at end of print()
           )")
           for d in api-c++ api-python developerguide userguide; do
             echo "::group:: Check ${d}"

examples/README.md

@@ -15,6 +15,10 @@ reading from:
 - GROMACS format files (see `python-examples/simulateGromacs.py`)
 - PDB (Protein Data Bank) files (to be used with OpenMM-compatible force fields; see `python-examples/simulatePdb.py`)
 
+These examples can also be found in the
+[Running Simulations chapter](https://docs.openmm.org/latest/userguide/application/02_running_sims.html)
+of the user guide, along with explanations of how they work.
+
 ### C++ API examples
 
 The examples in `cpp-examples` demonstrate the use of OpenMM's C++ API, and also
@@ -25,4 +29,4 @@ show how to use its C and Fortran bindings.  For more information, see
 
 You can also find:
 - [Extra utility scripts](extras/README.md) in `extras`
-- A suite of benchmarks for OpenMM in `Benchmarks`
+- A suite of benchmarks for OpenMM in `benchmarks`