Merge branch 'ckhrulev/packaging' into dev

pism · Feb 27, 2024 · 6cbfee2 · 6cbfee2
2 parents bcbab6e + 714b4af
commit 6cbfee2
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -131,7 +131,7 @@ jobs:
             mkdir -p build
             cmake -B build -S doc/
             make -C build manual_html
-            mv build/sphinx/html ./manual_html
+            mv build/sphinx/manual_html ./manual_html
       - persist_to_workspace:
           root: .
           paths: manual_html
@@ -271,6 +271,64 @@ jobs:
             --message "Update the source code browser"
             --dist doxygen
 
+  build-and-test-with-ubuntu-libs:
+    docker:
+      - image: ckhrulev/pism-ubuntu-deb-package:0.1.1
+
+    environment:
+      CC: mpicc
+      CXX: mpicxx
+      OMPI_ALLOW_RUN_AS_ROOT: 1
+      OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+
+    steps:
+      - checkout
+      - run:
+          name: Configure PISM
+          command: >-
+            cmake -S . -B build
+            -DCMAKE_BUILD_TYPE=Debug
+            -DPism_BUILD_EXTRA_EXECS=YES
+            -DPism_USE_PROJ=YES
+      - run:
+          name: Build PISM
+          command: make --no-print-directory -C build -j ${N:-4} package
+      - run:
+          name: Test PISM
+          command: cd build && ctest -j ${N:-4} --output-on-failure
+
+  build-deb-package:
+    docker:
+      - image: ckhrulev/pism-ubuntu-deb-package:0.1.1
+
+    environment:
+      CC: mpicc
+      CXX: mpicxx
+
+    steps:
+      - checkout
+      - run:
+          name: Configure PISM
+          command: >-
+            cmake -S . -B build
+            -DCMAKE_BUILD_TYPE=Release
+            -DCMAKE_INSTALL_PREFIX=/usr
+            -DPism_BUILD_DOCS=YES
+            -DPism_BUILD_EXTRA_EXECS=NO
+            -DPism_BUILD_PYTHON_BINDINGS=NO
+            -DPism_USE_PROJ=YES
+      - run:
+          name: Build PISM
+          command: make --no-print-directory -C build -j ${N:-4} package
+      - run:
+          name: Move the package
+          command: mkdir -p /tmp/package && mv build/*.deb /tmp/package/
+      - run:
+          name: Test the package
+          command: lintian /tmp/package/*.deb
+      - store_artifacts:
+          path: /tmp/package
+
 workflows:
   version: 2
   build-and-test:
@@ -336,6 +394,8 @@ workflows:
       - manual-html
       - manual-pdf
       - doxygen
+      - build-and-test-with-ubuntu-libs
+      - build-deb-package
 
       - deploy-p:
           requires:

diff --git a/CMake/PISM_CMake_macros.cmake b/CMake/PISM_CMake_macros.cmake
@@ -22,10 +22,7 @@ endmacro(pism_use_rpath)
 
 # Set CMake variables to disable rpath
 macro(pism_dont_use_rpath)
-  set (CMAKE_SKIP_BUILD_RPATH TRUE)
-  set (CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
-  set (CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_FULL_LIBDIR}")
-  set (CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)
+  set (CMAKE_SKIP_INSTALL_RPATH TRUE)
 endmacro(pism_dont_use_rpath)
 
 # Set CMake variables to ensure that everything is static
@@ -48,31 +45,16 @@ macro(pism_strictly_static)
   pism_dont_use_rpath()
 endmacro(pism_strictly_static)
 
-# Set Pism_VERSION, Pism_VERSION_LONG
-macro(pism_set_revision_tag)
+# Set Pism_VERSION_LONG
+macro(pism_set_full_version)
   if (EXISTS ${Pism_SOURCE_DIR}/.git)
     # get version information from the repository
     find_program (GIT_EXECUTABLE git DOC "Git executable")
     mark_as_advanced(GIT_EXECUTABLE)
-    # Get the current branch
-    execute_process (COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD
+    execute_process (COMMAND ${GIT_EXECUTABLE} rev-parse --short HEAD
       WORKING_DIRECTORY ${Pism_SOURCE_DIR}
-      OUTPUT_VARIABLE Pism_BRANCH
+      OUTPUT_VARIABLE Pism_COMMIT_HASH
       OUTPUT_STRIP_TRAILING_WHITESPACE)
-    if (${Pism_BRANCH} MATCHES "main")
-      # Get the latest tag
-      execute_process (COMMAND ${GIT_EXECUTABLE} describe --always --match v?.?*
-        WORKING_DIRECTORY ${Pism_SOURCE_DIR}
-        OUTPUT_VARIABLE Pism_VERSION
-        OUTPUT_STRIP_TRAILING_WHITESPACE)
-      # remove "v" from vX.Y.Z:
-      string(REPLACE "v" "" Pism_VERSION ${Pism_VERSION})
-    else()
-      execute_process (COMMAND ${GIT_EXECUTABLE} rev-parse --short HEAD
-        WORKING_DIRECTORY ${Pism_SOURCE_DIR}
-        OUTPUT_VARIABLE Pism_VERSION
-        OUTPUT_STRIP_TRAILING_WHITESPACE)
-    endif()
     execute_process (COMMAND ${GIT_EXECUTABLE} --no-pager log -1 "--pretty=format:%an"
       WORKING_DIRECTORY ${Pism_SOURCE_DIR}
       OUTPUT_VARIABLE Pism_COMMIT_AUTHOR
@@ -81,21 +63,13 @@ macro(pism_set_revision_tag)
       WORKING_DIRECTORY ${Pism_SOURCE_DIR}
       OUTPUT_VARIABLE Pism_COMMIT_DATE
       OUTPUT_STRIP_TRAILING_WHITESPACE)
-    if (${Pism_BRANCH} MATCHES "main")
-      set(Pism_VERSION_LONG "${Pism_VERSION} committed by ${Pism_COMMIT_AUTHOR}")
-    else()
-      set(Pism_VERSION_LONG "${Pism_COMMIT_DATE}-${Pism_VERSION} committed by ${Pism_COMMIT_AUTHOR}")
-    endif()
-  elseif(EXISTS ${Pism_SOURCE_DIR}/VERSION)
-    # No repository info: we are probably building from a tarball
-    file(STRINGS ${Pism_SOURCE_DIR}/VERSION Pism_VERSION LIMIT_COUNT 1)
-    set(Pism_VERSION_LONG "${Pism_VERSION}")
+    set(Pism_VERSION_LONG "${Pism_VERSION}-${Pism_COMMIT_HASH} committed by ${Pism_COMMIT_AUTHOR} on ${Pism_COMMIT_DATE}")
   else()
-    set (Pism_VERSION "unknown")
-  endif (EXISTS ${Pism_SOURCE_DIR}/.git)
+    set(Pism_VERSION_LONG "${Pism_VERSION}")
+  endif()
 
   message(STATUS "PISM version: '${Pism_VERSION_LONG}'")
-endmacro(pism_set_revision_tag)
+endmacro(pism_set_full_version)
 
 # Set pedantic compiler flags
 macro(pism_set_pedantic_flags)

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,11 +1,33 @@
 cmake_minimum_required (VERSION 3.16)
-project (Pism C CXX)
+
+# Get PISM's "short" X.Y.Z version from a file
+if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/VERSION)
+  file(STRINGS ${CMAKE_CURRENT_SOURCE_DIR}/VERSION Pism_VERSION LIMIT_COUNT 1)
+else()
+  message(FATAL_ERROR "'VERSION' not found: cannot determine PISM's version")
+endif()
+
+project (Pism
+  VERSION ${Pism_VERSION}
+  HOMEPAGE_URL "https://www.pism.io"
+  LANGUAGES C CXX)
+
+include ("CMake/PISM_CMake_macros.cmake")
+list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMake")
+pism_set_full_version()
 
 include (GNUInstallDirs)
 # doc directory: override capitalization ("pism" instead of "Pism" from the "project(...)"
 # call above)
 set(CMAKE_INSTALL_DOCDIR ${CMAKE_INSTALL_DATAROOTDIR}/doc/pism)
 
+if ((EXISTS "/etc/debian_version") AND ("${CMAKE_INSTALL_PREFIX}" MATCHES "/usr"))
+  message(STATUS "Installing in /usr on Debian or Ubuntu (we are probably building a package)")
+  set(Pism_DEBIAN_SYSTEMWIDE YES)
+else()
+  set(Pism_DEBIAN_SYSTEMWIDE NO)
+endif()
+
 # Deal with build types
 mark_as_advanced(CLEAR CMAKE_BUILD_TYPE)
 # Set the build type to "Release" so that users get optimized code by default:
@@ -39,11 +61,6 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
   add_compile_options(-fstandalone-debug)
 endif()
 
-include ("CMake/PISM_CMake_macros.cmake")
-list (APPEND CMAKE_MODULE_PATH "${Pism_SOURCE_DIR}/CMake")
-
-pism_set_revision_tag()
-
 # Put executables in the build directory:
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
 
@@ -85,7 +102,11 @@ option (Pism_PEDANTIC_WARNINGS  "Compile with pedantic warnings." ON)
 option (Pism_GPROF_FLAGS        "Add flags necessary to profile with gprof." OFF)
 
 # Use rpath by default; this has to go first, because rpath settings may be overridden later.
-pism_use_rpath()
+if (Pism_DEBIAN_SYSTEMWIDE)
+  pism_dont_use_rpath()
+else()
+  pism_use_rpath()
+endif()
 
 if (Pism_LINK_STATICALLY)
   pism_strictly_static()
@@ -155,18 +176,31 @@ if (Pism_BUILD_PYTHON_BINDINGS)
   mark_as_advanced (SWIG_DIR SWIG_EXECUTABLE SWIG_VERSION)
 
   set (pism_python_path_py "${CMAKE_CURRENT_BINARY_DIR}/pism_python_path.py")
+  if (Pism_DEBIAN_SYSTEMWIDE)
+    set (pism_sysconfig_scheme "deb_system")
+  else()
+    set (pism_sysconfig_scheme "posix_prefix")
+  endif()
   file (WRITE "${pism_python_path_py}" "
 # Get module installation path from Python:
 import sysconfig
-print(sysconfig.get_path('platlib', 'posix_prefix', vars={'platbase': '${CMAKE_INSTALL_PREFIX}'}))
+print(sysconfig.get_path('platlib', '${pism_sysconfig_scheme}', vars={'platbase': '${CMAKE_INSTALL_PREFIX}'}))
 ")
+  unset(pism_sysconfig_scheme)
 
   execute_process(
     COMMAND ${PYTHON_EXECUTABLE} ${pism_python_path_py}
-    OUTPUT_VARIABLE PISM_INSTALL_PYTHON_MODULE_DIR
+    OUTPUT_VARIABLE PISM_FULL_PYTHON_MODULE_DIR
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  set(PISM_INSTALL_PYTHON_MODULE_DIR ${PISM_INSTALL_PYTHON_MODULE_DIR}
+  # convert to a path relative to the install prefix
+  file(RELATIVE_PATH PISM_PYTHON_MODULE_DIR
+    ${CMAKE_INSTALL_PREFIX} ${PISM_FULL_PYTHON_MODULE_DIR})
+  unset(pism_python_path_py)
+  set(PISM_PYTHON_MODULE_DIR ${PISM_PYTHON_MODULE_DIR}
     CACHE PATH "Python extension module installation directory." )
+  set(PISM_FULL_PYTHON_MODULE_DIR ${PISM_FULL_PYTHON_MODULE_DIR}
+    CACHE PATH "Python extension module installation directory (full path)." )
+  mark_as_advanced(PISM_PYTHON_MODULE_DIR PISM_FULL_PYTHON_MODULE_DIR)
 endif ()
 
 add_custom_target (etags
@@ -200,11 +234,18 @@ install(PROGRAMS
   util/nc2cdo.py
   util/nccmp.py
   util/plot_profiling.py
-  DESTINATION ${CMAKE_INSTALL_BINDIR})
+  DESTINATION ${CMAKE_INSTALL_DATADIR}/pism/bin)
 
 install(DIRECTORY ${PROJECT_SOURCE_DIR}/examples
-  DESTINATION ${CMAKE_INSTALL_DATADIR}/pism
-  USE_SOURCE_PERMISSIONS)
+  DESTINATION ${CMAKE_INSTALL_DATADIR}/doc/pism
+  DIRECTORY_PERMISSIONS
+  OWNER_EXECUTE OWNER_WRITE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE WORLD_READ
+  PATTERN .gitignore EXCLUDE
+  PATTERN __pycache__ EXCLUDE
+  PATTERN "*.pyc" EXCLUDE
+  PATTERN "*.nc" EXCLUDE
+  PATTERN "*.npz" EXCLUDE
+  PATTERN "*~" EXCLUDE)
 
 add_subdirectory (src)
 add_subdirectory (site-packages)
@@ -224,3 +265,5 @@ add_subdirectory (test)
 add_subdirectory (test/regression)
 
 add_subdirectory (docker)
+
+add_subdirectory (package)
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.2-dev
+2.1.99
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
@@ -15,7 +15,13 @@ if (NOT Pism_SOURCE_DIR)
 
   include ("${Pism_SOURCE_DIR}/CMake/PISM_CMake_macros.cmake")
 
-  pism_set_revision_tag()
+  if(EXISTS ${Pism_SOURCE_DIR}/VERSION)
+    file(STRINGS ${Pism_SOURCE_DIR}/VERSION Pism_VERSION LIMIT_COUNT 1)
+  else()
+    message(FATAL_ERROR "'VERSION' not found: cannot determine PISM's version")
+  endif()
+
+  pism_set_full_version()
 
   include (GNUInstallDirs)
 endif()
@@ -27,3 +33,5 @@ if (DOXYGEN_EXECUTABLE AND DOXYGEN_DOT_EXECUTABLE)
   # Source code browser:
   add_subdirectory (browser EXCLUDE_FROM_ALL)
 endif ()
+
+add_subdirectory(manpages)
diff --git a/doc/manpages/CMakeLists.txt b/doc/manpages/CMakeLists.txt
@@ -0,0 +1,26 @@
+find_program(RST2MAN_EXECUTABLE NAMES rst2man rst2man.py)
+mark_as_advanced(RST2MAN_EXECUTABLE)
+
+if (RST2MAN_EXECUTABLE)
+  find_package(UnixCommands)
+  macro(add_manpages names)
+    foreach(name ${names})
+      # Note the sed command: this fixes formatting of command-line options: rst2man
+      # cannot handle PISM's long options with one dash.
+      add_custom_command(OUTPUT ${name}.1.gz
+        COMMAND ${RST2MAN_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${name}.rst ${name}.1
+        COMMAND sed -i -E -e "s/(-[a-zA-Z]+)\\\\fB /\\1/" ${name}.1
+        COMMAND ${GZIP} -n -9 ${name}.1
+        DEPENDS ${name}.rst
+        VERBATIM)
+
+      install(FILES
+        ${CMAKE_CURRENT_BINARY_DIR}/${name}.1.gz
+        DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+    endforeach(name)
+  endmacro(add_manpages)
+
+  add_manpages("pismr;pismv")
+
+  add_custom_target(manpages ALL DEPENDS pismr.1.gz pismv.1.gz)
+endif()
diff --git a/doc/manpages/README.md b/doc/manpages/README.md
@@ -0,0 +1,5 @@
+This directory contains very basic manpages for most important PISM executables.
+
+To build manpages, make sure that your system has `rst2man` in the `PATH` (on
+Debian/Ubuntu this requires `python3-docutils`) and set `Pism_BUILD_DOCS` to "on" using
+CMake.
diff --git a/doc/manpages/pismr.rst b/doc/manpages/pismr.rst
@@ -0,0 +1,42 @@
+=====
+pismr
+=====
+
+------------------------------------------------
+Parallel Ice Sheet Model (PISM): prognostic runs
+------------------------------------------------
+:Author: [email protected]
+:Date:   2024-2-21
+:Copyright: Copyright (C) 2024 Constantine Khrulev
+:Version: 0.1
+:Manual section: 1
+:Manual group: science
+
+SYNOPSIS
+========
+
+|  pismr -i *input_file.nc* ...
+|  pismr -boot_file *bootstrapping_file.nc* ...
+
+DESCRIPTION
+===========
+
+``pismr`` performs an evolution run using PISM, a Parallel Ice Sheet Model. Please see the
+*PISM User's Manual* for details.
+
+OPTIONS
+=======
+
+-i          input file
+-bootstrap  enables bootstrapping mode
+-y          run length, in model years
+-o          output file name
+-help       prints PISM and PETSc command-line option help; use with **grep**
+-verbose    selects stdout verbosity level, 1 -- minimal output, 2 -- normal, 3 -- more debugging info, ...
+
+SEE ALSO
+========
+
+- The *User's Manual* and other documentation online at https://www.pism.io/docs/manual
+
+- **pismv** to run some verification tests