Merge branch 'dials:main' into h5_table_format

.azure-pipelines/unix-build-cmake.yml

@@ -28,7 +28,7 @@ steps:
     dials-data
     pytest-cov
     pytest-timeout" >> modules/dials/${{ parameters.conda_environment }}
-    python modules/dials/installer/bootstrap.py base --clean --python $(PYTHON_VERSION) --cmake
+    python modules/dials/installer/bootstrap.py base --clean --python $(PYTHON_VERSION)
   displayName: Create python $(PYTHON_VERSION) environment
   workingDirectory: $(Pipeline.Workspace)
 
@@ -37,7 +37,9 @@ steps:
 
 # Build and install dxtbx
 - script: |
-    source activate conda_base/
+    source conda_base/etc/profile.d/conda.sh
+    conda activate conda_base/
+    set -euo pipefail
     git clone https://github.com/cctbx/dxtbx ./modules/dxtbx
     mkdir build_dxtbx
     cd build_dxtbx
@@ -52,8 +54,10 @@ steps:
 
 # Build DIALS using the bootstrap script
 - bash: |
-    source activate conda_base/
-    set -eux
+    source conda_base/etc/profile.d/conda.sh
+    conda activate conda_base/
+    set -euxo pipefail
+    set -x
     export CXXFLAGS="-isystem$(Pipeline.Workspace)/conda_base ${CXXFLAGS:-}"
     mkdir build_dials
     cd build_dials
@@ -68,7 +72,9 @@ steps:
 
 # Extract the dials-data version so we can correctly cache regression data.
 - bash: |
-    source activate conda_base/
+    source conda_base/etc/profile.d/conda.sh
+    conda activate conda_base/
+    set -euxo pipefail
     echo "##vso[task.setvariable variable=DIALS_DATA_VERSION_FULL]$(dials.data info -v | grep version.full)"
     echo "##vso[task.setvariable variable=DIALS_DATA_VERSION]$(dials.data info -v | grep version.major_minor)"
     mkdir -p data
@@ -97,7 +103,8 @@ steps:
 
 # Finally, run the full regression test suite
 - bash: |
-    source activate conda_base/
+    source conda_base/etc/profile.d/conda.sh
+    conda activate conda_base/
     set -eux
     export DIALS_DATA=${PWD}/data
     export PYTHONDEVMODE=1

.azure-pipelines/unix-build.yml

@@ -17,14 +17,14 @@ steps:
 # Download source repositories using the bootstrap script
 - bash: |
     set -eux
-    python modules/dials/installer/bootstrap.py update
+    python modules/dials/installer/bootstrap.py update --libtbx
   displayName: Repository checkout
   workingDirectory: $(Pipeline.Workspace)
 
 # Create a new conda environment using the bootstrap script
 - script: |
     set -eux
-    python modules/dials/installer/bootstrap.py base --clean --python $(PYTHON_VERSION)
+    python modules/dials/installer/bootstrap.py base --clean --python $(PYTHON_VERSION) --libtbx
   displayName: Create python $(PYTHON_VERSION) environment
   workingDirectory: $(Pipeline.Workspace)
 
@@ -46,7 +46,7 @@ steps:
 - bash: |
     set -eux
     export CXXFLAGS="-isystem$(Pipeline.Workspace)/conda_base ${CXXFLAGS:-}"
-    python modules/dials/installer/bootstrap.py build --config-flags=--use_environment_flags
+    python modules/dials/installer/bootstrap.py build --config-flags=--use_environment_flags --libtbx
   displayName: DIALS build
   workingDirectory: $(Pipeline.Workspace)
 
@@ -94,7 +94,7 @@ steps:
     # A conflict between new setuptools and matplotlib causes test failures due to warnings in subprocesses
     export PYTHONWARNINGS='ignore:pkg_resources is deprecated as an API:DeprecationWarning,ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning'
     cd modules/dials
-    pytest -v -ra -n auto --basetemp="$(Pipeline.Workspace)/tests" --durations=10 --dist loadgroup\
+    libtbx.python -m pytest -v -ra -n auto --basetemp="$(Pipeline.Workspace)/tests" --durations=10 --dist loadgroup\
         --cov=$(pwd) --cov-report=html --cov-report=xml --cov-branch \
         --timeout=5400 --regression || echo "##vso[task.complete result=Failed;]Some tests failed"
   displayName: Run tests

.azure-pipelines/windows-build.yml

@@ -29,7 +29,7 @@ steps:
 
     mv ci-conda-env.txt modules/dials/.conda-envs/windows.txt
 
-    python3 modules/dials/installer/bootstrap.py base --clean --python $(PYTHON_VERSION) --cmake
+    python3 modules/dials/installer/bootstrap.py base --clean --python $(PYTHON_VERSION)
 
   displayName: Create python $(PYTHON_VERSION) environment
   workingDirectory: $(Pipeline.Workspace)

.conda-envs/linux.txt

@@ -1,57 +1,57 @@
-conda-forge::alabaster
-conda-forge::biopython
-conda-forge::bzip2
-conda-forge::c-compiler
-conda-forge::colorlog
-conda-forge::conda
-conda-forge::cxx-compiler
-conda-forge::dials-data>=2.4.72
-conda-forge::docutils
-conda-forge::eigen
-conda-forge::future
-conda-forge::gemmi>=0.6.5
-conda-forge::h5py>=3.1.0
-conda-forge::hdf5
-conda-forge::hdf5plugin
-conda-forge::iota
-conda-forge::jinja2
-conda-forge::libboost-devel
-conda-forge::libboost-python-devel
-conda-forge::libglu
-conda-forge::matplotlib-base>=3.0.2
-conda-forge::mesa-libgl-devel-cos7-x86_64
-conda-forge::mrcfile
-conda-forge::msgpack-cxx
-conda-forge::msgpack-python
-conda-forge::natsort
-conda-forge::numpy>=1.21.5,<2
-conda-forge::nxmx
-conda-forge::orderedset
-conda-forge::pandas
-conda-forge::pillow>=5.4.1
-conda-forge::pint
-conda-forge::pip
-conda-forge::psutil
-conda-forge::pybind11
-conda-forge::pyopengl
-conda-forge::pyrtf
-conda-forge::pytest
-conda-forge::pytest-forked
-conda-forge::pytest-mock
-conda-forge::pytest-xdist
-conda-forge::python-dateutil>=2.7.0
-conda-forge::reportlab
-conda-forge::requests
-conda-forge::scikit-learn
-conda-forge::scipy
-conda-forge::scons
-conda-forge::setuptools
-conda-forge::six
-conda-forge::sphinx>=4
-conda-forge::sqlite
-conda-forge::tabulate
-conda-forge::tqdm
-conda-forge::urllib3
-conda-forge::wxpython>=4.2.0
-conda-forge::xz
-conda-forge::zlib
+alabaster
+biopython
+bzip2
+c-compiler
+colorlog
+conda
+cxx-compiler
+dials-data>=2.4.72
+docutils
+eigen
+future
+gemmi>=0.6.5
+h5py>=3.1.0
+hdf5
+hdf5plugin
+iota
+jinja2
+libboost-devel
+libboost-python-devel
+libglu
+matplotlib-base>=3.0.2
+mesa-libgl-devel-cos7-x86_64
+mrcfile
+msgpack-cxx
+msgpack-python
+natsort
+numpy>=1.21.5,<2
+nxmx
+orderedset
+pandas
+pillow>=5.4.1
+pint
+pip
+psutil
+pybind11
+pyopengl
+pyrtf
+pytest
+pytest-forked
+pytest-mock
+pytest-xdist
+python-dateutil>=2.7.0
+reportlab
+requests
+scikit-learn
+scipy
+scons
+setuptools
+six
+sphinx>=4
+sqlite
+tabulate
+tqdm
+urllib3
+wxpython>=4.2.0
+xz
+zlib

.conda-envs/macos.txt

@@ -1,58 +1,58 @@
-conda-forge::alabaster
-conda-forge::biopython
-conda-forge::bzip2
-conda-forge::c-compiler
-conda-forge::colorlog
-conda-forge::conda
-conda-forge::cxx-compiler
-conda-forge::dials-data>=2.4.72
-conda-forge::docutils
-conda-forge::eigen
-conda-forge::future
-conda-forge::gemmi>=0.6.5
-conda-forge::h5py>=3.1.0
-conda-forge::hdf5
-conda-forge::hdf5plugin
-conda-forge::iota
-conda-forge::jinja2
-conda-forge::libboost-devel
-conda-forge::libboost-python-devel
-conda-forge::libcxx
-conda-forge::matplotlib-base>=3.0.2
-conda-forge::mrcfile
-conda-forge::msgpack-cxx
-conda-forge::msgpack-python
-conda-forge::natsort
-conda-forge::numpy>=1.21.5,<2
-conda-forge::nxmx
-conda-forge::orderedset
-conda-forge::pandas
-conda-forge::pillow>=5.4.1
-conda-forge::pint
-conda-forge::pip
-conda-forge::psutil
-conda-forge::pthread-stubs
-conda-forge::pybind11
-conda-forge::pyopengl
-conda-forge::pyrtf
-conda-forge::pytest
-conda-forge::pytest-forked
-conda-forge::pytest-mock
-conda-forge::pytest-xdist
-conda-forge::python-dateutil>=2.7.0
-conda-forge::python.app
-conda-forge::reportlab
-conda-forge::requests
-conda-forge::scikit-learn
-conda-forge::scipy
-conda-forge::scons
-conda-forge::setuptools
-conda-forge::six
-conda-forge::sphinx>=4
-conda-forge::sqlite
-conda-forge::tabulate
-conda-forge::tqdm
-conda-forge::urllib3
-conda-forge::wxpython>=4.2.0=*_5
-conda-forge::xz
-conda-forge::zlib
+alabaster
+biopython
+bzip2
+c-compiler
+colorlog
+conda
+cxx-compiler
+dials-data>=2.4.72
+docutils
+eigen
+future
+gemmi>=0.6.5
+h5py>=3.1.0
+hdf5
+hdf5plugin
+iota
+jinja2
+libboost-devel
+libboost-python-devel
+libcxx
+matplotlib-base>=3.0.2
+mrcfile
+msgpack-cxx
+msgpack-python
+natsort
+numpy>=1.21.5,<2
+nxmx
+orderedset
+pandas
+pillow>=5.4.1
+pint
+pip
+psutil
+pthread-stubs
+pybind11
+pyopengl
+pyrtf
+pytest
+pytest-forked
+pytest-mock
+pytest-xdist
+python-dateutil>=2.7.0
+python.app
+reportlab
+requests
+scikit-learn
+scipy
+scons
+setuptools
+six
+sphinx>=4
+sqlite
+tabulate
+tqdm
+urllib3
+wxpython>=4.2.0=*_5
+xz
+zlib