Update CI images

.gitlab-ci.yml

@@ -58,7 +58,7 @@ style:
 style_doxygen:
   <<: *global_job_definition
   stage: prepare
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:01cf23487c9eeec758daf425c9947d8089ed9da0
   dependencies: []
   script:
     - mkdir build
@@ -107,7 +107,7 @@ no_rotation:
 debian:10:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/debian:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/debian:446ff604bbfa63f30ddb462697fa0d0dc2630460
   script:
     - export with_cuda=false
     - export myconfig=maxset make_check_python=false
@@ -119,7 +119,7 @@ debian:10:
 opensuse:15.1:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/opensuse:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/opensuse:446ff604bbfa63f30ddb462697fa0d0dc2630460
   script:
     - export with_cuda=false myconfig=maxset make_check_python=false
     - bash maintainer/CI/build_cmake.sh
@@ -130,7 +130,7 @@ opensuse:15.1:
 centos:7:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/centos:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/centos:446ff604bbfa63f30ddb462697fa0d0dc2630460
   script:
     - export with_cuda=false myconfig=maxset make_check_python=true
     - bash maintainer/CI/build_cmake.sh
@@ -141,20 +141,32 @@ centos:7:
 fedora:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/fedora:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/fedora:446ff604bbfa63f30ddb462697fa0d0dc2630460
   script:
     - export with_cuda=false myconfig=maxset make_check_python=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
     - linux
 
+fedora:latest:
+  <<: *global_job_definition
+  stage: build
+  image: docker.pkg.github.com/espressomd/docker/fedora:latest_base
+  script:
+    - export with_cuda=false myconfig=maxset make_check_python=false
+    - bash maintainer/CI/build_cmake.sh
+  tags:
+    - docker
+    - linux
+  when: manual
+
 ### Builds with CUDA
 
 cuda10-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:01cf23487c9eeec758daf425c9947d8089ed9da0
   script:
     - export myconfig=maxset with_coverage=false test_timeout=900 srcdir=${CI_PROJECT_DIR}
     - export cmake_params="-DIPYTHON_EXECUTABLE=$(which jupyter)"
@@ -171,7 +183,7 @@ cuda10-maxset:
 cuda9-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-9.0:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-9.0:01cf23487c9eeec758daf425c9947d8089ed9da0
   script:
     - export myconfig=maxset with_coverage=true test_timeout=900 srcdir=${CI_PROJECT_DIR}
     - sed -i 's/ or "DISPLAY" in os.environ/ or True/' src/python/espressomd/visualization.pyx
@@ -189,7 +201,7 @@ cuda9-maxset:
 tutorials-samples-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:01cf23487c9eeec758daf425c9947d8089ed9da0
   script:
     - export myconfig=maxset with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=false test_timeout=1200
@@ -202,7 +214,7 @@ tutorials-samples-maxset:
 tutorials-samples-default:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:01cf23487c9eeec758daf425c9947d8089ed9da0
   script:
     - export myconfig=default with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=false test_timeout=1200
@@ -217,7 +229,7 @@ tutorials-samples-default:
 tutorials-samples-empty:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:01cf23487c9eeec758daf425c9947d8089ed9da0
   script:
     - export myconfig=empty with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=false test_timeout=1200 with_scafacos=false
@@ -232,7 +244,7 @@ tutorials-samples-empty:
 tutorials-samples-no-gpu:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:01cf23487c9eeec758daf425c9947d8089ed9da0
   script:
     - export myconfig=maxset with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=false test_timeout=1200 hide_gpu=true
@@ -246,7 +258,7 @@ tutorials-samples-no-gpu:
 installation:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:01cf23487c9eeec758daf425c9947d8089ed9da0
   script:
     - export myconfig=maxset with_coverage=false make_check_unit_tests=false make_check_python=false
     - export srcdir=${CI_PROJECT_DIR} test_timeout=1800
@@ -289,7 +301,7 @@ empty:
 ubuntu:wo-dependencies:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:wo-dependencies
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-wo-dependencies:446ff604bbfa63f30ddb462697fa0d0dc2630460
   script:
     - export myconfig=maxset make_check_unit_tests=false make_check_python=false
     - bash maintainer/CI/build_cmake.sh
@@ -302,13 +314,24 @@ ubuntu:wo-dependencies:
 rocm-maxset:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/rocm-python3:latest
+  image: docker.pkg.github.com/espressomd/docker/rocm:446ff604bbfa63f30ddb462697fa0d0dc2630460
   script:
     - export myconfig=maxset
     - bash maintainer/CI/build_cmake.sh
   tags:
     - amdgpu
 
+rocm:latest:
+  <<: *global_job_definition
+  stage: build
+  image: docker.pkg.github.com/espressomd/docker/rocm:latest_base
+  script:
+    - export myconfig=maxset
+    - bash maintainer/CI/build_cmake.sh
+  tags:
+    - amdgpu
+  when: manual
+
 ### Builds with OS X
 
 osx:
@@ -334,7 +357,7 @@ osx-cuda:
 clang:6.0:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/clang-python3:6.0
+  image: docker.pkg.github.com/espressomd/docker/clang:446ff604bbfa63f30ddb462697fa0d0dc2630460
   script:
     - export myconfig=maxset with_coverage=false with_static_analysis=true with_asan=true with_ubsan=true test_timeout=900
     - bash maintainer/CI/build_cmake.sh
@@ -363,7 +386,7 @@ intel:19:
 check_sphinx:
   <<: *global_job_definition
   stage: additional_checks
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:01cf23487c9eeec758daf425c9947d8089ed9da0
   needs:
     - cuda10-maxset
   when: on_success
@@ -384,7 +407,7 @@ check_sphinx:
 run_tutorials:
   <<: *global_job_definition
   stage: additional_checks
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:01cf23487c9eeec758daf425c9947d8089ed9da0
   needs:
     - cuda10-maxset
   when: on_success
@@ -408,7 +431,7 @@ run_tutorials:
 run_doxygen:
   <<: *global_job_definition
   stage: additional_checks
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:01cf23487c9eeec758daf425c9947d8089ed9da0
   needs:
     - cuda10-maxset
   when: on_success
@@ -428,7 +451,7 @@ run_doxygen:
 check_cuda_maxset_no_gpu:
   <<: *global_job_definition
   stage: additional_checks
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-9.0
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-9.0:01cf23487c9eeec758daf425c9947d8089ed9da0
   when: on_success
   needs: 
     - cuda9-maxset
@@ -444,7 +467,7 @@ check_cuda_maxset_no_gpu:
 check_with_odd_no_of_processors:
   <<: *global_job_definition
   stage: additional_checks 
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-9.0
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-9.0:01cf23487c9eeec758daf425c9947d8089ed9da0
   when: on_success
   needs: 
     - cuda9-maxset
@@ -461,12 +484,11 @@ check_with_odd_no_of_processors:
 .deploy_base:
   <<: *global_job_definition
   stage: deploy
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-9.0
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:e24415d47e2611662efe56b9946f1d0c1dda32d7
   only:
     - python
   before_script:
-    - 'which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )'
-    - eval $(ssh-agent -s)
+    - 'which ssh-agent && eval $(ssh-agent -s) || exit 1'
     - ssh-add <(echo "$SSH_PRIVATE_KEY")
     - mkdir -p ${HOME}/.ssh && chmod 700 ${HOME}/.ssh
     - echo "$SSH_PRIVATE_KEY" > ${HOME}/.ssh/espresso_rsa && chmod 600 ${HOME}/.ssh/espresso_rsa

.travis.yml

@@ -11,7 +11,7 @@ matrix:
     - os: linux
       sudo: required
       services: docker
-      env: myconfig=maxset image=ubuntu-python3
+      env: myconfig=maxset image=espressomd/docker-ubuntu-18.04:446ff604bbfa63f30ddb462697fa0d0dc2630460
 
 script:
   - maintainer/CI/build_docker.sh

doc/sphinx/conf.py.in

@@ -254,7 +254,7 @@ napoleon_use_param = False
 autodoc_mock_imports = ['featuredefs', 'matplotlib', 'OpenGL', 'mayavi', 'pyface', 'tvtk', 'vtk', 'MDAnalysis', 'electrostatics']
 
 def setup(app):
-    app.add_stylesheet('bibtex.css')
+    app.add_css_file('bibtex.css')
 
 
 # -- Options for Cython ---------------------------------------------------

maintainer/CI/build_docker.sh

@@ -30,8 +30,8 @@ make_check=${make_check}
 EOF
 
 if [ -z "${image}" ]; then
-    image="ubuntu"
+    echo "ERROR: environment variable 'image' is missing" >&2
+    exit 1
 fi
 
-image="espressomd/espresso-${image}:latest"
 docker run -u espresso --env-file "${ENV_FILE}" -v "${PWD}:/travis" -it "${image}" /bin/bash -c "cp -r /travis .; cd travis && maintainer/CI/build_cmake.sh" || exit 1

requirements.txt

@@ -18,7 +18,7 @@ traitsui>=4.5.1
 requests>=2.9.1 # to post on GitHub as espresso-ci
 lxml>=3.5.0 # to deploy tutorials
 # sphinx and its dependencies
-sphinx>=1.6.6,!=2.1.0
+sphinx>=1.6.6,!=2.1.0,!=3.0.0
 sphinxcontrib-bibtex>=0.3.5
 # pep8 and its dependencies
 autopep8==1.3.4

src/python/espressomd/accumulators.py

@@ -34,11 +34,6 @@ class MeanVarianceCalculator(ScriptInterfaceHelper):
     -------
     update()
         Update the accumulator (get the current values from the observable).
-    get_mean()
-        Returns the samples mean values of the respective observable with which the
-        accumulator was initialized.
-    get_variance()
-        Returns the samples variance for the observable.
 
     """
     _so_name = "Accumulators::MeanVarianceCalculator"
@@ -49,9 +44,16 @@ class MeanVarianceCalculator(ScriptInterfaceHelper):
     _so_creation_policy = "LOCAL"
 
     def get_mean(self):
+        """
+        Returns the samples mean values of the respective observable with
+        which the accumulator was initialized.
+        """
         return np.array(self.call_method("get_mean")).reshape(self.shape())
 
     def get_variance(self):
+        """
+        Returns the samples variance for the observable.
+        """
         return np.array(self.call_method("get_variance")).reshape(self.shape())
 
 
@@ -71,8 +73,6 @@ class TimeSeries(ScriptInterfaceHelper):
     -------
     update()
         Update the accumulator (get the current values from the observable).
-    time_series()
-        Returns the recorded values of the observable.
     clear()
         Clear the data
 
@@ -86,6 +86,9 @@ class TimeSeries(ScriptInterfaceHelper):
     _so_creation_policy = "LOCAL"
 
     def time_series(self):
+        """
+        Returns the recorded values of the observable.
+        """
         return np.array(self.call_method("time_series")).reshape(self.shape())
 
 

src/python/espressomd/constraints.py

@@ -555,8 +555,6 @@ class HomogeneousFlowField(Constraint):
 
     Attributes
     ----------
-    u : (3,) array_like of :obj:`float`
-        Field velocity.
     gamma : :obj:`float`
         Coupling constant
 
@@ -569,6 +567,12 @@ def __init__(self, **kwargs):
 
     @property
     def u(self):
+        """
+        Returns
+        -------
+        (3,) array_like of :obj:`float` :
+            Field velocity.
+        """
         return self.value
 
     _so_name = "Constraints::HomogeneousFlowField"

src/python/espressomd/drude_helpers.py

@@ -38,7 +38,7 @@ def add_drude_particle_to_core(system, harmonic_bond, thermalized_bond,
     Collects types/charges/polarizations/Thole factors for intramolecular
     core-Drude short-range exclusion and Thole interaction.
 
-    Attributes
+    Parameters
     ----------
 
     system : :class:`espressomd.system.System`
@@ -135,7 +135,7 @@ def add_thole_pair_damping(system, t1, t2, verbose=False):
     Calculates mixed Thole factors depending on Thole damping and polarization.
     Adds non-bonded Thole interactions to the system.
 
-    Attributes
+    Parameters
     ----------
 
     system : :class:`espressomd.system.System`
@@ -164,7 +164,7 @@ def add_all_thole(system, verbose=False):
     Calls :meth:`add_thole_pair_damping()` for all necessary combinations to
     create the interactions.
 
-    Attributes
+    Parameters
     ----------
 
     system : :class:`espressomd.system.System`
@@ -195,7 +195,7 @@ def setup_and_add_drude_exclusion_bonds(system, verbose=False):
     between Drude particles and core charges and adds the bonds to the cores.
     Has to be called once after all Drude particles have been created.
 
-    Attributes
+    Parameters
     ----------
 
     system : :class:`espressomd.system.System`
@@ -236,7 +236,7 @@ def setup_intramol_exclusion_bonds(system, mol_drude_types, mol_core_types,
     between Drude particles and partial charges of the cores. Has to be called once
     after all Drude particles have been created.
 
-    Attributes
+    Parameters
     ----------
 
     system : :class:`espressomd.system.System`
@@ -275,7 +275,7 @@ def add_intramol_exclusion_bonds(system, drude_ids, core_ids, verbose=False):
     Applies electrostatic short-range exclusion bonds for the given ids.
     Has to be applied for all molecules.
 
-    Attributes
+    Parameters
     ----------
 
     system : :class:`espressomd.system.System`