Remove/replace many mentions of Jenkins

diff --git a/cmake/gmxManageFFTLibraries.cmake b/cmake/gmxManageFFTLibraries.cmake
index e412641fcec82b742f79991a9282151f65bd7083..77e931a3e3b4834d9f0fac24a0f81ef5795f22b3 100644 (file)
--- a/cmake/gmxManageFFTLibraries.cmake
+++ b/cmake/gmxManageFFTLibraries.cmake
@@ -130,9 +130,6 @@ elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
     if (NOT MKL_MANUALLY)
         # The next line takes care of everything for MKL
         if (WIN32)
     if (NOT MKL_MANUALLY)
         # The next line takes care of everything for MKL
         if (WIN32)

-            # This works according to the Intel MKL 10.3 for Windows
-            # docs, but on Jenkins Win2k8, icl tries to interpret it
-            # as a file. Shrug.

             set(FFT_LINKER_FLAGS "/Qmkl:sequential")
         elseif(GMX_INTEL_LLVM AND GMX_INTEL_LLVM_VERSION GREATER_EQUAL 2021020)
             set(FFT_LINKER_FLAGS "-qmkl=sequential")
             set(FFT_LINKER_FLAGS "/Qmkl:sequential")
         elseif(GMX_INTEL_LLVM AND GMX_INTEL_LLVM_VERSION GREATER_EQUAL 2021020)
             set(FFT_LINKER_FLAGS "-qmkl=sequential")

diff --git a/docs/dev-manual/releng/jenkins-howto.rst b/docs/dev-manual/releng/jenkins-howto.rst
deleted file mode 100644 (file)
index e32ba1c..0000000
--- a/docs/dev-manual/releng/jenkins-howto.rst
+++ /dev/null
@@ -1,11 +0,0 @@
-.. This file is a placeholder that is used in case RELENG_PATH does not
-   identify the location of the releng repository.
-
-.. _jenkins-howto:
-
-jenkins howto (missing)
-===========================
-
-This documentation was built without releng documentation.
-If you want to see this documentation, set ``RELENG_PATH`` CMake variable to
-point to the root of a checkout from the releng repository.

diff --git a/docs/dev-manual/releng/jenkins-ui.rst b/docs/dev-manual/releng/jenkins-ui.rst
deleted file mode 100644 (file)
index bcf9d9d..0000000
--- a/docs/dev-manual/releng/jenkins-ui.rst
+++ /dev/null
@@ -1,11 +0,0 @@
-.. This file is a placeholder that is used in case RELENG_PATH does not
-   identify the location of the releng repository.
-
-.. _jenkins-ui:
-
-jenkins ui (missing)
-===========================
-
-This documentation was built without releng documentation.
-If you want to see this documentation, set ``RELENG_PATH`` CMake variable to
-point to the root of a checkout from the releng repository.

diff --git a/docs/doxygen/CMakeLists.txt b/docs/doxygen/CMakeLists.txt
index 232adc044b70e9dd631fe1a3b545f4b7aee5a7e0..6de85e4f6633f8dcf3f15c812003138310742125 100644 (file)
--- a/docs/doxygen/CMakeLists.txt
+++ b/docs/doxygen/CMakeLists.txt
@@ -119,7 +119,7 @@ if (DOXYGEN_FOUND)
     else()
         # If there is no git, we just update the stamp every time, and the
         # builds are triggered every time.  This should be rare enough, but
     else()
         # If there is no git, we just update the stamp every time, and the
         # builds are triggered every time.  This should be rare enough, but

-        # this case still needs to be supported for the Jenkins job that builds
+        # this case still needs to be supported for the CI job that builds

         # the documentation for a release from the release tarball.
         gmx_add_custom_output_target(doxygen-source-timestamp
             RUN_ALWAYS OUTPUT STAMP
         # the documentation for a release from the release tarball.
         gmx_add_custom_output_target(doxygen-source-timestamp
             RUN_ALWAYS OUTPUT STAMP


@@ -207,7 +207,7 @@ if (DOXYGEN_FOUND)
         # TODO: Consider whether this is the best location for this code,
         # since not all of it is Doxygen-specific (but nearly all of it
         # relies on the Doxygen XML documentation).
         # TODO: Consider whether this is the best location for this code,
         # since not all of it is Doxygen-specific (but nearly all of it
         # relies on the Doxygen XML documentation).

-        # The output .log file currently needs to be here, since Jenkins
+        # The output .log file currently needs to be here, since CI

         # expects that.
         set(check_source_command
             ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/check-source.py
         # expects that.
         set(check_source_command
             ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/check-source.py

diff --git a/docs/doxygen/RunDoxygen.cmake.cmakein b/docs/doxygen/RunDoxygen.cmake.cmakein
index d7910d366dade7af7c2e6612a76978ba6c0c585a..da8c85bd9d38c76984417303ae94edc81a212338 100644 (file)
--- a/docs/doxygen/RunDoxygen.cmake.cmakein
+++ b/docs/doxygen/RunDoxygen.cmake.cmakein
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
 #
 # This file is part of the GROMACS molecular simulation package.
 #

-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2021, by the GROMACS development team, led by

 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.


@@ -62,12 +62,12 @@ if (DOXYGEN_WARNINGS)
     message("The following warnings were produced by Doxygen:")
     message("${STRIPPED_WARNINGS}")
     # Remove some useless/hard-to-suppress warnings from the file to avoid
     message("The following warnings were produced by Doxygen:")
     message("${STRIPPED_WARNINGS}")
     # Remove some useless/hard-to-suppress warnings from the file to avoid

-    # Jenkins complaining.
+    # CI complaining.

     string(REGEX REPLACE
            "warning:[^\n]*Consider increasing DOT_GRAPH_MAX_NODES.\n" ""
            DOXYGEN_WARNINGS "${DOXYGEN_WARNINGS}")
     # Add a note to the warnings that identify the documentation type that
     string(REGEX REPLACE
            "warning:[^\n]*Consider increasing DOT_GRAPH_MAX_NODES.\n" ""
            DOXYGEN_WARNINGS "${DOXYGEN_WARNINGS}")
     # Add a note to the warnings that identify the documentation type that

-    # produces them.  This makes it easier to see in Jenkins if a warning type
+    # produces them.  This makes it easier to see in CI if a warning type

     # is produced only from some documentation types.
     string(REGEX REPLACE "\n" " (in doxygen-${DOCTYPE})\n"
            DOXYGEN_WARNINGS "${DOXYGEN_WARNINGS}")
     # is produced only from some documentation types.
     string(REGEX REPLACE "\n" " (in doxygen-${DOCTYPE})\n"
            DOXYGEN_WARNINGS "${DOXYGEN_WARNINGS}")

diff --git a/docs/linkcheckerrc b/docs/linkcheckerrc
index 312237512cdf795a1040714cdca10f07ec52d2ae..5d9755753a024a6b5d8db50f59c0b7575d5738df 100644 (file)
--- a/docs/linkcheckerrc
+++ b/docs/linkcheckerrc
@@ -8,7 +8,3 @@ ignore=
  cmake.org
 # This site gives warnings because it redirects to itself
  http://swift.cmbi.ru.nl/gv/dssp
  cmake.org
 # This site gives warnings because it redirects to itself
  http://swift.cmbi.ru.nl/gv/dssp

-# This site has a robots.txt that denies access
- jenkins.gromacs.org
-# A matching regressiontests tarball generally can't be found on this server yet.
- gerrit.gromacs.org/download

diff --git a/python_packaging/docker/README.md b/python_packaging/docker/README.md
index b149784a69fc24409e7c86da278c7b1e37cfd8fd..13b7ec7931cceb57a82ec36174dae4ebe63e6464 100644 (file)
--- a/python_packaging/docker/README.md
+++ b/python_packaging/docker/README.md
@@ -2,7 +2,7 @@
 
 This directory segregates the Dockerfiles to avoid clutter. The Dockerfiles
 here help to build and test gmxapi software. They may be subsumed or supplanted
 
 This directory segregates the Dockerfiles to avoid clutter. The Dockerfiles
 here help to build and test gmxapi software. They may be subsumed or supplanted

-by future Jenkins infrastructure.
+by future infrastructure.

 
 Assume you have already checked out the commit you want to build for.
 Assume the following definitions.
 
 Assume you have already checked out the commit you want to build for.
 Assume the following definitions.


@@ -129,7 +129,7 @@ Then browse to http://localhost:8080/
 
 ## Automation
 
 
 ## Automation
 

-*TODO: Update this section as Jenkins infrastructure evolves.*
+*TODO: Update this section as CI infrastructure evolves.*

 
 Travis-CI builds and pushes a chain of Docker images to the `gmxapi` dockerhub organization.
 The `kassonlab` GitHub organization `gromacs-gmxapi` repository branches that are descended from the `kassonLabFork`
 
 Travis-CI builds and pushes a chain of Docker images to the `gmxapi` dockerhub organization.
 The `kassonlab` GitHub organization `gromacs-gmxapi` repository branches that are descended from the `kassonLabFork`

diff --git a/share/template/CMakeLists.txt b/share/template/CMakeLists.txt
index 00828e711cdf8d63a1116c7e1c11a15ef5ac0e3a..706641db279ee6fb347cfb8242720181af9ee4ef 100644 (file)
--- a/share/template/CMakeLists.txt
+++ b/share/template/CMakeLists.txt
@@ -2,7 +2,7 @@
 # This file is part of the GROMACS molecular simulation package.
 #
 # Copyright (c) 2011,2012,2014,2016,2018 by the GROMACS development team.
 # This file is part of the GROMACS molecular simulation package.
 #
 # Copyright (c) 2011,2012,2014,2016,2018 by the GROMACS development team.

-# Copyright (c) 2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by

 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.


@@ -44,7 +44,7 @@ target_include_directories(template SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/ext
 target_link_libraries(template libgromacs legacy_modules ${GMX_EXE_LINKER_FLAGS})
 
 set(DOCUMENTATION_HTTP_URL_BASE
 target_link_libraries(template libgromacs legacy_modules ${GMX_EXE_LINKER_FLAGS})
 
 set(DOCUMENTATION_HTTP_URL_BASE

-    http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc)
+    https://manual.gromacs.org/nightly/index.html)

 if (SOURCE_IS_SOURCE_DISTRIBUTION)
     set(DOCUMENTATION_HTTP_URL_BASE
         http://manual.gromacs.org/documentation/${GMX_VERSION_STRING})
 if (SOURCE_IS_SOURCE_DISTRIBUTION)
     set(DOCUMENTATION_HTTP_URL_BASE
         http://manual.gromacs.org/documentation/${GMX_VERSION_STRING})

diff --git a/src/gromacs/timing/wallcycle.cpp b/src/gromacs/timing/wallcycle.cpp
index 12d5f376d0f33727800eaf78d7e68844e2f1e0da..1f1d7ca38ea2eec6b6ac4f68f2505d530ed0e163 100644 (file)
--- a/src/gromacs/timing/wallcycle.cpp
+++ b/src/gromacs/timing/wallcycle.cpp
@@ -720,8 +720,8 @@ void wallcycle_print(FILE*                            fplog,
            code so that it is provably robust with respect to
            non-positive values for all possible timer and cycle
            counters, there is less value gained from printing whatever
            code so that it is provably robust with respect to
            non-positive values for all possible timer and cycle
            counters, there is less value gained from printing whatever

-           timing data might still be sensible for some non-Jenkins
-           run, than is lost from diagnosing Jenkins FP exceptions on
+           timing data might still be sensible for some non-CI
+           run, than is lost from diagnosing CI FP exceptions on

            runs about whose execution time we don't care. */
         GMX_LOG(mdlog.warning)
                 .asParagraph()
            runs about whose execution time we don't care. */
         GMX_LOG(mdlog.warning)
                 .asParagraph()

diff --git a/src/gromacs/utility/baseversion_gen.h b/src/gromacs/utility/baseversion_gen.h
index 0249270ec41ac5dc0c01be2dcd94717e1e4b1dd9..1d225237dffa41f2086864514f90844eb09486d2 100644 (file)
--- a/src/gromacs/utility/baseversion_gen.h
+++ b/src/gromacs/utility/baseversion_gen.h
@@ -58,7 +58,7 @@ extern const char gmx_central_base_hash[];
  *
  *  The variable is populated with the generated DOI string
  *  by CMake when the build of a release version is
  *
  *  The variable is populated with the generated DOI string
  *  by CMake when the build of a release version is

- *  requested by Jenkins. Allows identification and
+ *  requested. Allows identification and

  *  referencing of different \Gromacs releases.
  */
 extern const char gmxSourceDoiString[];
  *  referencing of different \Gromacs releases.
  */
 extern const char gmxSourceDoiString[];

diff --git a/src/programs/legacymodules.cpp b/src/programs/legacymodules.cpp
index 467f6a2f4947e3c0220400965d7a716b163f08a7..b145559efc49cc0b18cd7cc7f6fef0b4a831c256 100644 (file)
--- a/src/programs/legacymodules.cpp
+++ b/src/programs/legacymodules.cpp
@@ -108,8 +108,8 @@ private:
         std::fprintf(stderr,
                      "This tool is no longer present in GROMACS. Please see\n"
                      "  "
         std::fprintf(stderr,
                      "This tool is no longer present in GROMACS. Please see\n"
                      "  "

-                     "http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/"
-                     "user-guide/cmdline.html#command-changes\n"
+                     "https://manual.gromacs.org/current/user-guide/"
+                     "cmdline.html#command-changes-between-versions\n"

                      "for ideas how to perform the same tasks with the "
                      "new tools.\n");
     }
                      "for ideas how to perform the same tasks with the "
                      "new tools.\n");
     }