Python maintenance

.github/workflows/push_pull.yml

@@ -16,7 +16,7 @@ jobs:
  - name: Setup Python environment
  uses: actions/setup-python@v2
  with:
- python-version: '3.7'
+ python-version: '3.8'
  - name: Check without sanitizer
  uses: ./.github/actions/build_and_check
  with:
@@ -33,7 +33,7 @@ jobs:
  - name: Setup Python environment
  uses: actions/setup-python@v2
  with:
- python-version: '3.7'
+ python-version: '3.8'
  - name: Check with sanitizer
  uses: ./.github/actions/build_and_check
  with:

.gitlab-ci.yml

@@ -21,7 +21,9 @@ stages:
  timeout: 40m
  interruptible: false
  tags:
- - linux
+ - docker
+ - espresso
+ - no-cuda
 
 variables:
  GIT_SUBMODULE_STRATEGY: recursive
@@ -44,7 +46,8 @@ style:
  - sh maintainer/CI/fix_style.sh
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
  variables:
  GIT_SUBMODULE_STRATEGY: none
  artifacts:
@@ -65,7 +68,8 @@ style_doxygen:
  - sh ../maintainer/CI/dox_warnings.sh
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
 
 ### Builds without CUDA
 
@@ -85,7 +89,8 @@ default:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
 
 maxset:
  <<: *global_job_definition
@@ -105,7 +110,9 @@ maxset:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
+ - numa
 
 no_rotation:
  <<: *global_job_definition
@@ -122,7 +129,9 @@ no_rotation:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
+ - numa
 
 ubuntu:wo-dependencies:
  <<: *global_job_definition
@@ -138,7 +147,8 @@ ubuntu:wo-dependencies:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
 
 ### Builds with different distributions
 
@@ -155,7 +165,8 @@ debian:10:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
 
 fedora:34:
  <<: *global_job_definition
@@ -170,7 +181,8 @@ fedora:34:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
 
 ### Builds with CUDA
 
@@ -195,8 +207,9 @@ clang-sanitizer:
  timeout: 2h
  tags:
  - docker
- - linux
+ - espresso
  - cuda
+ - numa
 
 fast_math:
  <<: *global_job_definition
@@ -215,7 +228,7 @@ fast_math:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
  - cuda
  when: manual
 
@@ -238,8 +251,9 @@ cuda11-maxset:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
  - cuda
+ - numa
 
 cuda10-maxset:
  <<: *global_job_definition
@@ -263,8 +277,9 @@ cuda10-maxset:
  expire_in: 1 week
  tags:
  - docker
- - linux
+ - espresso
  - cuda
+ - numa
 
 tutorials-samples-maxset:
  <<: *global_job_definition
@@ -287,7 +302,7 @@ tutorials-samples-maxset:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
  - cuda
 
 tutorials-samples-default:
@@ -310,7 +325,7 @@ tutorials-samples-default:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
  - cuda
  only:
  - schedules
@@ -336,7 +351,7 @@ tutorials-samples-empty:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
  - cuda
  only:
  - schedules
@@ -362,7 +377,8 @@ tutorials-samples-no-gpu:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
  only:
  - schedules
 
@@ -397,7 +413,7 @@ installation:
  - make -j2 check_tutorials
  tags:
  - docker
- - linux
+ - espresso
  - cuda
  when: manual
 
@@ -417,8 +433,9 @@ empty:
  - bash maintainer/CI/build_cmake.sh
  tags:
  - docker
- - linux
+ - espresso
  - cuda
+ - numa
 
 check_sphinx:
  <<: *global_job_definition
@@ -440,8 +457,9 @@ check_sphinx:
  expire_in: 1 week
  tags:
  - docker
- - linux
+ - espresso
  - cuda
+ - numa
 
 run_tutorials:
  <<: *global_job_definition
@@ -464,8 +482,9 @@ run_tutorials:
  expire_in: 1 week
  tags:
  - docker
- - linux
+ - espresso
  - cuda
+ - numa
  only:
  - schedules
 
@@ -486,7 +505,9 @@ run_doxygen:
  expire_in: 1 week
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
+ - numa
 
 maxset_no_gpu:
  <<: *global_job_definition
@@ -500,7 +521,9 @@ maxset_no_gpu:
  - make -t && make check
  tags:
  - docker
- - linux
+ - espresso
+ - no-cuda
+ - numa
 
 maxset_3_cores:
  <<: *global_job_definition
@@ -514,8 +537,9 @@ maxset_3_cores:
  - make -t && make check_unit_tests && make check_python_parallel_odd
  tags:
  - docker
- - linux
+ - espresso
  - cuda
+ - numa
 
 status_success:
  <<: *notification_job_definition

CMakeLists.txt

@@ -170,7 +170,7 @@ if(WITH_CUDA)
  endif()
 endif(WITH_CUDA)
 
-find_package(PythonInterp 3.7 REQUIRED)
+find_package(PythonInterp 3.8 REQUIRED)
 
 if(WITH_PYTHON)
  find_package(Cython 0.29.14 REQUIRED)

doc/sphinx/inter_bonded.rst

@@ -399,6 +399,9 @@ angle between the planes defined by the particle triples :math:`p_1`,
 Together with appropriate Lennard-Jones interactions, this potential can
 mimic a large number of atomic torsion potentials.
 
+Note that there is a singularity in the forces, but not in the energy, when
+:math:`\phi = 0` and :math:`\phi = \pi`.
+
 
 Tabulated dihedral potential
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -414,6 +417,8 @@ A tabulated dihedral interaction can be instantiated via
 The energy and force tables must be sampled from :math:`0` to :math:`2\pi`.
 For details of the interpolation, see :ref:`Tabulated interaction`.
 
+Note that there is a singularity in the forces, but not in the energy, when
+:math:`\phi = 0` and :math:`\phi = \pi`.
 
 .. _Immersed Boundary Method interactions:
 

doc/sphinx/system_setup.rst

@@ -158,7 +158,7 @@ Lees--Edwards boundary conditions
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Lees--Edwards boundary conditions (LEbc) are special periodic boundary
-conditions to simulation systems under shear stress :cite:`lees72a`.
+conditions to simulate systems under shear stress :cite:`lees72a`.
 Periodic images of particles across the shear boundary appear with a
 time-dependent position offset. When a particle crosses the shear boundary,
 it appears to the opposite side of the simulation box with a position offset
@@ -227,13 +227,13 @@ The properties of the cell system can be accessed by
 
 * :py:attr:`~espressomd.cellsystem.CellSystem.node_grid`
 
- (int[3]) 3D node grid for real space domain decomposition (optional, if
+ 3D node grid for real space domain decomposition (optional, if
  unset an optimal set is chosen automatically). The domain decomposition
  can be visualized with :file:`samples/visualization_cellsystem.py`.
 
 * :py:attr:`~espressomd.cellsystem.CellSystem.skin`
 
- (float) Skin for the Verlet list. This value has to be set, otherwise the simulation will not start.
+ Skin for the Verlet list. This value has to be set, otherwise the simulation will not start.
 
 Details about the cell system can be obtained by :meth:`espressomd.system.System.cell_system.get_state() <espressomd.cellsystem.CellSystem.get_state>`:
 

maintainer/CI/build_cmake.sh

@@ -72,6 +72,12 @@ set_default_value() {
  fi
 }
 
+# the number of available processors depends on the CI runner
+if grep -q "i7-3820" /proc/cpuinfo; then
+ ci_procs=2
+else
+ ci_procs=4
+fi
 
 # handle environment variables
 set_default_value srcdir "$(pwd)"
@@ -82,7 +88,7 @@ set_default_value with_ubsan false
 set_default_value with_asan false
 set_default_value with_static_analysis false
 set_default_value myconfig "default"
-set_default_value build_procs 2
+set_default_value build_procs ${ci_procs}
 set_default_value check_procs ${build_procs}
 set_default_value check_odd_only false
 set_default_value check_gpu_only false

maintainer/CI/deploy_tutorials.py

@@ -20,20 +20,18 @@
 
 """List all tutorial files to deploy (PDF, HTML and figures)"""
 
-import os
-import glob
+import pathlib
 import lxml.html
 
-deploy_list = glob.glob('*/*.pdf')
-for filepath in glob.glob('*/*.html'):
+deploy_list = list(pathlib.Path().glob('*/*.pdf'))
+for filepath in pathlib.Path().glob('*/*.html'):
  deploy_list.append(filepath)
  # extract all figures
- dirname = os.path.dirname(filepath)
  with open(filepath, encoding='utf-8') as f:
  html = lxml.html.parse(f)
  figures = filter(lambda src: not src.startswith('data:image'),
  html.xpath('//img/@src'))
- deploy_list += list(map(lambda src: os.path.join(dirname, src), figures))
+ deploy_list += list(map(lambda src: filepath.parent / src, figures))
 
 with open('deploy_list.txt', 'w') as f:
- f.write('\n'.join(deploy_list))
+ f.write('\n'.join(map(str, deploy_list)))

maintainer/CI/dox_warnings.py

@@ -18,7 +18,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 #
 import re
-import os
+import pathlib
 
 # collect list of Doxygen warnings
 with open('doc/doxygen/warnings.log') as f:
@@ -38,7 +38,7 @@
  for line in content.strip().split('\n'):
  m = re.search(r'^(.+):(\d+):[\s\*]*([@\\]t?param).*\s(\S+)\s*$', line)
  filepath, lineno, paramtype, varname = m.groups()
- ext = os.path.splitext(filepath)[1]
+ ext = pathlib.Path(filepath).suffix
  if ext.lower() not in source_code_ext:
  continue
  warning = (f'argument \'{varname}\' of {paramtype} has no description,'