Merge pull request #163 from neutrinoceros/test_python_311

TST: test on Python 3.11

.circleci/config.yml

@@ -10,7 +10,6 @@ commands:
             echo 'export GOLD_STANDARD=HEAD' >> $BASH_ENV
             echo 'export ROCKSTAR_DIR=$HOME/rockstar-galaxies' >> $BASH_ENV
             echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROCKSTAR_DIR' >> $BASH_ENV
-            echo 'export YT_DIR=$HOME/yt-git' >> $BASH_ENV
             echo 'export YT_DATA=$HOME/yt_test' >> $BASH_ENV
             echo 'export TEST_DIR=$HOME/test_results' >> $BASH_ENV
             echo 'export TEST_NAME=astro_analysis' >> $BASH_ENV
@@ -46,24 +45,26 @@ commands:
             pip install --upgrade pip
             pip install mpi4py
             export MAX_BUILD_CORES=2
-            # install yt from source
-            if [ ! -f $YT_DIR/README.md ]; then
-                git clone --branch=main https://github.com/yt-project/yt $YT_DIR
-            fi
-            pushd $YT_DIR
-            git pull origin main
-            git checkout main
-            pip install .
-            popd
+            python -m pip install git+https://github.com/yt-project/yt
+
+            export YT_ASTRO_DIR=$(pwd)
             # install rockstar
             sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 100
             if [ ! -f $ROCKSTAR_DIR/VERSION ]; then
                 git clone https://bitbucket.org/pbehroozi/rockstar-galaxies $ROCKSTAR_DIR
                 pushd $ROCKSTAR_DIR
+
+                # apply patches necessary for compat with Ubuntu 22.04
+                git apply $YT_ASTRO_DIR/rockstar-patches/cflags.patch --whitespace=fix
+
                 make lib
                 popd
             fi
             echo $ROCKSTAR_DIR > rockstar.cfg
+
+            # never attempt to build h5py from source
+            pip install h5py --only-binary h5py
+
             # install yt_astro_analysis with extra dev dependencies
             pip install .[dev]
             # configure yt
@@ -196,7 +197,7 @@ jobs:
 
   run-tests-pytest:
     # Run a subset of the test suite (yield-based tests are not supported by pytest)
-    # this is necessary to test in Python 3.10 because it's not compatible with nose
+    # this is necessary to test in Python 3.10+ because it's not compatible with nose
     parameters:
       tag:
         type: string
@@ -299,6 +300,10 @@ workflows:
            name: "Python 3.10 tests"
            tag: "3.10.0"
 
+       - run-tests-pytest:
+           name: "Python 3.11 tests"
+           tag: "3.11.1"
+
        - docs-test:
            name: "Test docs build"
            tag: "3.9.7"

rockstar-patches/cflags.patch

@@ -0,0 +1,24 @@
+diff --git a/Makefile b/Makefile
+index 66f7e17..debd222 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,7 +1,7 @@
+-CFLAGS=-m64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_BSD_SOURCE -D_POSIX_SOURCE -D_POSIX_C_SOURCE=200809L -D_SVID_SOURCE -D_DARWIN_C_SOURCE -Wall -fno-math-errno -fPIC
++CFLAGS=-m64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_POSIX_C_SOURCE=200809L -D_DEFAULT_SOURCE -D_DARWIN_C_SOURCE -Wall -fno-math-errno -fPIC -I/usr/include/tirpc
+ LDFLAGS=-shared
+ OFLAGS = -lm -O3 -std=c99
+-DEBUGFLAGS = -lm -g -O3 -std=c99 #-Dinline=
++DEBUGFLAGS = -lm -g -O3 -std=c99 #-Dinline=
+ PROFFLAGS = -lm -g -pg -O2 -std=c99
+ CC = gcc
+ CFILES = rockstar.c check_syscalls.c fof.c groupies.c subhalo_metric.c potential.c nfw.c jacobi.c fun_times.c interleaving.c universe_time.c hubble.c integrate.c distance.c config_vars.c config.c bounds.c inthash.c io/read_config.c client.c server.c merger.c inet/socket.c inet/rsocket.c inet/address.c io/meta_io.c io/io_internal.c io/io_ascii.c io/stringparse.c io/io_gadget.c io/io_generic.c io/io_art.c io/io_nchilada.c io/io_tipsy.c io/io_bgc2.c io/io_util.c io/io_arepo.c io/io_hdf5.c io/io_enzo.c
+diff --git a/examples/Makefile b/examples/Makefile
+index caf2322..a192fe5 100644
+--- a/examples/Makefile
++++ b/examples/Makefile
+@@ -1,4 +1,4 @@
+-CFLAGS=-m64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_BSD_SOURCE -D_POSIX_SOURCE -D_POSIX_C_SOURCE=200809L -D_SVID_SOURCE -D_DARWIN_C_SOURCE -lm -fno-math-errno -Wall
++CFLAGS=-m64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_POSIX_C_SOURCE=200809L -D_DEFAULT_SOURCE -D_DARWIN_C_SOURCE -lm -fno-math-errno -Wall
+ OFLAGS = -O3 -std=c99
+ DEBUGFLAGS = -g -O3 -std=c99
+ PROFFLAGS = -g -pg -O2 -std=c99