Update to IMP 2.22.0, drop Python 2

.github/workflows/build.yml

@@ -15,10 +15,6 @@ jobs:
         os: [ubuntu-latest]
         python-version: ["3.12"]
         imp-branch: [main, develop]
-        include:
-        - os: [ubuntu-latest]
-          python-version: "2.7"
-          imp-branch: main
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -37,8 +33,7 @@ jobs:
         source ${CONDA_PREFIX}/etc/conda/activate.d/activate-gxx_linux-64.sh
         cd modules/foo
         mkdir build && cd build
-        if test "${{ matrix.python-version }}" = "2.7" ; then PY2=on; else PY2=off; fi
-        cmake .. -DIMP_DIR=${CONDA_PREFIX}/lib/cmake/IMP -DUSE_PYTHON2=${PY2} -DCMAKE_CXX_FLAGS="-fprofile-arcs -ftest-coverage"
+        cmake .. -DIMP_DIR=${CONDA_PREFIX}/lib/cmake/IMP -DCMAKE_CXX_FLAGS="-fprofile-arcs -ftest-coverage"
         make
         ./setup_environment.sh pytest --cov=.. --cov-branch --cov-report=xml -v ../test/test_*.py test/*/*.py
         ${GCC/gcc/gcov} $(find . -name "*.gcno")

doc/valgrind.ipynb

@@ -61,7 +61,7 @@
       "source": [
         "# Build procedure<a id=\"build\"></a>\n",
         "\n",
-        "To build the custom module, either drop the entire module into IMP's `modules` directory and then build IMP from source code [in the usual way](https://integrativemodeling.org/2.21.0/doc/manual/installation.html#installation_compilation), or build the module [out of tree](https://integrativemodeling.org/2.21.0/doc/manual/outoftree.html) pointing CMake to an existing IMP installation. In order for Valgrind to be maximally useful, build the module with extra debugging information available by passing `-DCMAKE_CXX_FLAGS=\"-g\"` to CMake. The module should build without errors (or even warnings) with gcc."
+        "To build the custom module, either drop the entire module into IMP's `modules` directory and then build IMP from source code [in the usual way](https://integrativemodeling.org/2.22.0/doc/manual/installation.html#installation_compilation), or build the module [out of tree](https://integrativemodeling.org/2.22.0/doc/manual/outoftree.html) pointing CMake to an existing IMP installation. In order for Valgrind to be maximally useful, build the module with extra debugging information available by passing `-DCMAKE_CXX_FLAGS=\"-g\"` to CMake. The module should build without errors (or even warnings) with gcc."
       ]
     },
     {
@@ -145,7 +145,7 @@
         " - In more complex programs with multiple code paths it can be tricky to make sure that every `new` is paired  with a `delete` and that we never try to free the same memory more than once.\n",
         " \n",
         "\n",
-        "In this case where the object is small it would be better to avoid dynamic memory allocation entirely and just create the `ScoreCalculator` object as an automatic variable (on the stack) as `ScoreCalculator calc(d, k_);` For a larger object, derive from the [IMP::Object](https://integrativemodeling.org/2.21.0/doc/ref/classIMP_1_1Object.html) class and use a [smart pointer](https://en.wikipedia.org/wiki/Smart_pointer) to make sure it gets cleaned up automatically (replacing `new` with `IMP_NEW` and using `IMP::Pointer` rather than raw C++ pointers).\n",
+        "In this case where the object is small it would be better to avoid dynamic memory allocation entirely and just create the `ScoreCalculator` object as an automatic variable (on the stack) as `ScoreCalculator calc(d, k_);` For a larger object, derive from the [IMP::Object](https://integrativemodeling.org/2.22.0/doc/ref/classIMP_1_1Object.html) class and use a [smart pointer](https://en.wikipedia.org/wiki/Smart_pointer) to make sure it gets cleaned up automatically (replacing `new` with `IMP_NEW` and using `IMP::Pointer` rather than raw C++ pointers).\n",
         "\n",
         "(Valgrind also reports some small memory leaks from IMP's SWIG interface. These aren't worth worrying about, since this is not our code, and they should be one-time allocations, which get cleaned up at the end of the program anyway.)\n"
       ]

support/setup_ci.sh

@@ -18,24 +18,8 @@ if [ ${imp_branch} = "develop" ]; then
 else
   IMP_CONDA="imp"
 fi
-if [ ${python_version} = "2.7" ]; then
-  BOOST=""
-  pip="pip<=19.3.1"
-  # Python.h includes crypt.h, which is no longer provided by default
-  crypt="libxcrypt"
-else
-  BOOST="libboost-devel"
-  pip="pip"
-  crypt=""
-fi
-conda create --yes -q -n python${python_version} -c salilab python=${python_version} ${pip} ${crypt} ${IMP_CONDA} ${BOOST} gxx_linux-64 eigen cereal swig cmake numpy
+conda create --yes -q -n python${python_version} -c salilab python=${python_version} pip ${IMP_CONDA} libboost-devel gxx_linux-64 eigen cereal swig cmake numpy
 eval "$(conda shell.bash hook)"
 conda activate python${python_version}
 
-if [ ${python_version} = "2.7" ]; then
-  # pytest-flake8 1.1.0 tries to import contextlib.redirect_stdout, which
-  # isn't present in Python 2
-  pip install pytest-cov coverage 'pytest-flake8<1.1'
-else
-  pip install pytest-cov coverage pytest-flake8
-fi
+pip install pytest-cov coverage pytest-flake8