Merge pull request #7 from hpc4cmb/pkg_update

Update packages and configs

.github/workflows/deploy.yml

@@ -32,38 +32,6 @@ jobs:
         run: docker tag hpc4cmb/cmbenv:${TAGNAME} hpc4cmb/cmbenv:latest
       - name: Push Docker Image
         run: echo "${DOCKER_PASSWORD}" | docker login -u "${DOCKER_USERNAME}" --password-stdin && docker push hpc4cmb/cmbenv:${TAGNAME} && docker push hpc4cmb/cmbenv:latest
-  toastdeps-py35:
-    name: TOAST Dependencies Python 3.5
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: Create Dockerfile
-        run: ./cmbenv -c docker-toastdeps-py35 -p /usr/local
-      - name: Set tag name
-        run: tag=$(echo "${GITHUB_REF}" | sed -e 's/.*\/\(v.*\)/\1/') && echo "::set-env name=TAGNAME::${tag}"
-      - name: Build Docker Image
-        run: docker build -t hpc4cmb/toast-deps-py35:${TAGNAME} -f Dockerfile_docker-toastdeps-py35 .
-      - name: Tag Latest
-        run: docker tag hpc4cmb/toast-deps-py35:${TAGNAME} hpc4cmb/toast-deps-py35:latest
-      - name: Push Docker Image
-        run: echo "${DOCKER_PASSWORD}" | docker login -u "${DOCKER_USERNAME}" --password-stdin && docker push hpc4cmb/toast-deps-py35:${TAGNAME} && docker push hpc4cmb/toast-deps-py35:latest
-  toastdeps-py36:
-    name: TOAST Dependencies Python 3.6
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: Create Dockerfile
-        run: ./cmbenv -c docker-toastdeps-py36 -p /usr/local
-      - name: Set tag name
-        run: tag=$(echo "${GITHUB_REF}" | sed -e 's/.*\/\(v.*\)/\1/') && echo "::set-env name=TAGNAME::${tag}"
-      - name: Build Docker Image
-        run: docker build -t hpc4cmb/toast-deps-py36:${TAGNAME} -f Dockerfile_docker-toastdeps-py36 .
-      - name: Tag Latest
-        run: docker tag hpc4cmb/toast-deps-py36:${TAGNAME} hpc4cmb/toast-deps-py36:latest
-      - name: Push Docker Image
-        run: echo "${DOCKER_PASSWORD}" | docker login -u "${DOCKER_USERNAME}" --password-stdin && docker push hpc4cmb/toast-deps-py36:${TAGNAME} && docker push hpc4cmb/toast-deps-py36:latest
   toastdeps-py37:
     name: TOAST Dependencies Python 3.7
     runs-on: ubuntu-latest
@@ -96,3 +64,20 @@ jobs:
         run: docker tag hpc4cmb/toast-deps-py38:${TAGNAME} hpc4cmb/toast-deps-py38:latest
       - name: Push Docker Image
         run: echo "${DOCKER_PASSWORD}" | docker login -u "${DOCKER_USERNAME}" --password-stdin && docker push hpc4cmb/toast-deps-py38:${TAGNAME} && docker push hpc4cmb/toast-deps-py38:latest
+  toastdeps-py39:
+    name: TOAST Dependencies Python 3.9
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Create Dockerfile
+        run: ./cmbenv -c docker-toastdeps-py39 -p /usr/local
+      - name: Set tag name
+        run: tag=$(echo "${GITHUB_REF}" | sed -e 's/.*\/\(v.*\)/\1/') && echo "::set-env name=TAGNAME::${tag}"
+      - name: Build Docker Image
+        run: docker build -t hpc4cmb/toast-deps-py39:${TAGNAME} -f Dockerfile_docker-toastdeps-py39 .
+      - name: Tag Latest
+        run: docker tag hpc4cmb/toast-deps-py39:${TAGNAME} hpc4cmb/toast-deps-py39:latest
+      - name: Push Docker Image
+        run: echo "${DOCKER_PASSWORD}" | docker login -u "${DOCKER_USERNAME}" --password-stdin && docker push hpc4cmb/toast-deps-py39:${TAGNAME} && docker push hpc4cmb/toast-deps-py39:latest
+

.github/workflows/test.yml

@@ -9,30 +9,6 @@ on:
     branches: [ master ]
 
 jobs:
-  py35:
-    name: Docker Py3.5 Debian
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: Create Dockerfile
-        run: ./cmbenv -c docker-py3.5-debian -p /usr/local
-      - name: Build Docker Image
-        run: docker build -t hpc4cmb/cmbenv:temp_py35 -f Dockerfile_docker-py3.5-debian .
-      - name: Test Docker Image
-        run: docker run hpc4cmb/cmbenv:temp_py35 python -c 'import toast.tests; toast.tests.run()' && docker run hpc4cmb/cmbenv:temp_py35 mpirun -np 2 python -c 'import toast.tests; toast.tests.run()'
-  py36:
-    name: Docker Py3.6 Debian
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: Create Dockerfile
-        run: ./cmbenv -c docker-py3.6-debian -p /usr/local
-      - name: Build Docker Image
-        run: docker build -t hpc4cmb/cmbenv:temp_py36 -f Dockerfile_docker-py3.6-debian .
-      - name: Test Docker Image
-        run: docker run hpc4cmb/cmbenv:temp_py36 python -c 'import toast.tests; toast.tests.run()' && docker run hpc4cmb/cmbenv:temp_py36 mpirun -np 2 python -c 'import toast.tests; toast.tests.run()'
   py37:
     name: Docker Py3.7 Debian
     runs-on: ubuntu-latest
@@ -57,3 +33,15 @@ jobs:
         run: docker build -t hpc4cmb/cmbenv:temp_py38 -f Dockerfile_docker-py3.8-debian .
       - name: Test Docker Image
         run: docker run hpc4cmb/cmbenv:temp_py38 python -c 'import toast.tests; toast.tests.run()' && docker run hpc4cmb/cmbenv:temp_py38 mpirun -np 2 python -c 'import toast.tests; toast.tests.run()'
+  py39:
+    name: Docker Py3.9 Debian
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Create Dockerfile
+        run: ./cmbenv -c docker-py3.9-debian -p /usr/local
+      - name: Build Docker Image
+        run: docker build -t hpc4cmb/cmbenv:temp_py39 -f Dockerfile_docker-py3.9-debian .
+      - name: Test Docker Image
+        run: docker run hpc4cmb/cmbenv:temp_py39 python -c 'import toast.tests; toast.tests.run()' && docker run hpc4cmb/cmbenv:temp_py39 mpirun -np 2 python -c 'import toast.tests; toast.tests.run()'

configs/cori-gcc

@@ -12,7 +12,7 @@ PYVERSION = 3.7
 PIP_PKGS =
 
 # Packages to install with conda
-CONDA_PKGS = future nose cython numpy scipy matplotlib pyyaml astropy six psutil ephem virtualenv pandas memory_profiler ipython cycler kiwisolver python-dateutil toml numba tbb nbstripout black wurlitzer ipympl ipykernel jupyterlab pyfftw pillow
+CONDA_PKGS = future nose cython numpy scipy matplotlib pyyaml astropy six psutil ephem virtualenv pandas memory_profiler ipython cycler kiwisolver python-dateutil toml numba tbb nbstripout black wurlitzer ipympl ipykernel jupyterlab pyfftw pillow pshmem tomlkit traitlets
 
 # Serial compilers
 
@@ -67,5 +67,5 @@ BOOSTCHAIN = gcc
 
 # Group and permissions to set
 
-CHGRP = hpcosmo
+CHGRP = cmb
 CHMOD = a+rX,g-w,o-w

configs/cori-gcc-gpu

@@ -12,7 +12,7 @@ PYVERSION = 3.7
 PIP_PKGS =
 
 # Packages to install with conda
-CONDA_PKGS = future nose cython numpy scipy matplotlib pyyaml astropy six psutil ephem virtualenv pandas memory_profiler ipython cycler kiwisolver python-dateutil toml numba tbb nbstripout black wurlitzer ipympl ipykernel jupyterlab pyfftw pillow
+CONDA_PKGS = future nose cython numpy scipy matplotlib pyyaml astropy six psutil ephem virtualenv pandas memory_profiler ipython cycler kiwisolver python-dateutil toml numba tbb nbstripout black wurlitzer ipympl ipykernel jupyterlab pyfftw pillow pshmem tomlkit traitlets
 
 # Serial compilers
 

configs/cori-gcc-gpu.pkgs

@@ -88,6 +88,9 @@ madam
 # Install SPT3G.  Frame based data format.
 #spt3g
 #
+# Install uncrustify
+uncrustify
+#
 # Install TIDAS.  HDF5-based timestream data format.
 #tidas
 #

configs/cori-gcc.pkgs

@@ -62,6 +62,9 @@ h5py
 # Install healpy
 healpy
 #
+# Install Pixell
+pixell
+#
 # Install quaternionarray
 qarray
 #
@@ -89,6 +92,9 @@ libflac
 # Install SPT3G.  Frame based data format.
 spt3g
 #
+# Install uncrustify
+uncrustify
+#
 # Install TIDAS.  HDF5-based timestream data format.
 tidas
 #

configs/cori-intel

@@ -12,7 +12,7 @@ PYVERSION = 3.7
 PIP_PKGS =
 
 # Packages to install with conda
-CONDA_PKGS = future nose cython numpy scipy matplotlib pyyaml astropy six psutil ephem virtualenv pandas memory_profiler ipython cycler kiwisolver python-dateutil toml numba tbb nbstripout black wurlitzer ipympl ipykernel jupyterlab pyfftw pillow
+CONDA_PKGS = future nose cython numpy scipy matplotlib pyyaml astropy six psutil ephem virtualenv pandas memory_profiler ipython cycler kiwisolver python-dateutil toml numba tbb nbstripout black wurlitzer ipympl ipykernel jupyterlab pyfftw pillow pshmem tomlkit traitlets
 
 # Serial compilers
 
@@ -64,9 +64,9 @@ LAPACK =
 
 # Boost toolchain name
 
-BOOSTCHAIN = intel-linux
+BOOSTCHAIN = gcc
 
 # Group and permissions to set
 
-CHGRP = hpcosmo
+CHGRP = cmb
 CHMOD = a+rX,g-w,o-w

configs/cori-intel.pkgs

@@ -62,6 +62,9 @@ h5py
 # Install healpy
 healpy
 #
+# Install Pixell
+pixell
+#
 # Install quaternionarray
 qarray
 #
@@ -87,7 +90,10 @@ madam
 libflac
 #
 # Install SPT3G.  Frame based data format.
-#spt3g
+spt3g
+#
+# Install uncrustify
+uncrustify
 #
 # Install TIDAS.  HDF5-based timestream data format.
 tidas

configs/docker-py3.7-debian

@@ -15,7 +15,7 @@ DOCKER_BASE = python:3.7-slim-buster
 DOCKER_SYS_PKGS = m4 libtool autoconf automake llvm libsuitesparse-dev libfftw3-dev libcfitsio-dev libflac-dev zlib1g-dev libbz2-dev libopenblas-dev liblapack-dev libhdf5-dev
 
 # Packages to install with pip
-PIP_PKGS = setuptools future six Cython cycler kiwisolver pyparsing python-dateutil toml pkgconfig pytz psutil==5.7.0 numpy==1.18.4 scipy==1.4.1 matplotlib==3.2.1 pandas==1.0.3 memory_profiler==0.57.0 astropy==4.0.1.post1 ephem==3.7.7.1 ipython==7.14.0 numba==0.49.1 tbb cmake sphinx sphinx-rtd-theme pyfftw
+PIP_PKGS = setuptools future six Cython cycler kiwisolver pyparsing python-dateutil toml pkgconfig pytz psutil==5.7.0 numpy==1.18.4 scipy==1.4.1 matplotlib==3.2.1 pandas==1.0.3 memory_profiler==0.57.0 astropy==4.0.1.post1 ephem==3.7.7.1 ipython==7.14.0 numba==0.49.1 tbb cmake sphinx sphinx-rtd-theme pyfftw pshmem tomlkit traitlets
 
 # Packages to install with conda
 CONDA_PKGS =