Squashed 'modules/pmi/' changes from abec8822a3..77f0301dd1

77f0301dd1 flake8 fix
c5f755d4c5 Clarify docs for offset, relates salilab/pmi#261
75e97da738 Update CI to use Python 3.12
c1cbfbc95b Newer Boost is only needed for Python 3 builds
c768064900 We now need Boost headers to build with IMP

git-subtree-dir: modules/pmi
git-subtree-split: 77f0301dd11bbec99cc47ca4c3a4897439df5fcd

modules/pmi/.github/workflows/build.yml

@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["2.7", "3.11"]
+        python-version: ["2.7", "3.12"]
     runs-on: ${{ matrix.os }}
 
     steps:

modules/pmi/pyext/src/topology/__init__.py

@@ -562,6 +562,12 @@ def add_structure(self, pdb_fn, chain_id, res_range=[],
                           is the ending residue index.
         @param offset     Apply an offset to the residue indexes of the PDB
                           file. This number is added to the PDB sequence.
+                          PMI uses 1-based FASTA numbering internally (the
+                          first residue in the sequence is numbered 1, and
+                          so on). If the PDB chain is not also numbered
+                          starting from 1, apply an offset to make it match
+                          the FASTA. For example, if the PDB is numbered
+                          starting from -5, use an offset of 6 (-5 + 6 = 1).
         @param model_num  Read multi-model PDB and return that model
         @param ca_only    Only read the CA positions from the PDB file
         @param soft_check If True, it only warns if there are sequence

modules/pmi/tools/setup_ci.sh

@@ -9,8 +9,13 @@ fi
 
 python_version=$1
 
+if [ ${python_version} = "2.7" ]; then
+  BOOST=""
+else
+  BOOST="libboost-devel"
+fi
 conda config --remove channels defaults  # get conda-forge, not main, packages
-conda create --yes -q -n python${python_version} -c salilab -c conda-forge python=${python_version} pip scipy matplotlib imp-nightly gxx_linux-64 eigen cereal swig cmake
+conda create --yes -q -n python${python_version} -c salilab -c conda-forge python=${python_version} pip scipy matplotlib imp-nightly ${BOOST} gxx_linux-64 eigen cereal swig cmake
 eval "$(conda shell.bash hook)"
 conda activate python${python_version}