Merge pull request #392 from sparcians/knutel/jerinjoy-clang-filesyst…

…em-fix

jerinjoy branch: clang filesystem fix; MacOS CI upgrade

.azure-pipelines/azure-pipelines-osx.yml

@@ -5,7 +5,7 @@
 jobs:
 - job: osx
   pool:
-    vmImage: macOS-10.15
+    vmImage: macOS-11
   strategy:
     matrix:
       osx_64_:
@@ -47,15 +47,6 @@ jobs:
     displayName: Prepare conda build artifacts
     condition: succeededOrFailed()
 
-  - task: PublishTestResults@2
-    condition: succeededOrFailed()
-    inputs:
-        testResultsFormat: 'cTest'
-        testResultsFiles: '**/Test.xml'
-        mergeTestResults: false # Unclear on impact of setting this true
-        failTaskOnFailedTests: true
-        publishRunAttachments: true # uploads xml files for possible inspection
-
   - task: PublishPipelineArtifact@1
     displayName: Store conda build artifacts
     condition: not(eq(variables.BLD_ARTIFACT_PATH, ''))

.ci_support/linux_64_.yaml

@@ -1,11 +1,11 @@
 boost:
-- 1.74.0
+- 1.78.0
 boost_cpp:
-- 1.74.0
+- 1.78.0
 c_compiler:
 - gcc
 c_compiler_version:
-- '10'
+- '11'
 cdt_name:
 - cos6
 channel_sources:
@@ -15,11 +15,11 @@ channel_targets:
 cxx_compiler:
 - gxx
 cxx_compiler_version:
-- '10'
+- '11'
 docker_image:
 - quay.io/condaforge/linux-anvil-cos7-x86_64
 hdf5:
-- 1.10.6
+- 1.12.2
 linux_clang_version:
 - '13'
 numpy:
@@ -32,8 +32,6 @@ pin_run_as_build:
   python:
     min_pin: x.x
     max_pin: x.x
-  sqlite:
-    max_pin: x
 python:
 - 3.8.* *_cpython
 sqlite:
@@ -45,3 +43,5 @@ zip_keys:
   - cxx_compiler_version
 - - python
   - numpy
+zlib:
+- '1.2'

.ci_support/osx_64_.yaml

@@ -1,27 +1,25 @@
 MACOSX_DEPLOYMENT_TARGET:
-- '10.13'
+- '11.1'
 boost:
-- 1.74.0
+- 1.78.0
 boost_cpp:
-- 1.74.0
+- 1.78.0
 c_compiler:
 - clang
 c_compiler_version:
-- '12'
+- '14'
 channel_sources:
 - conda-forge
 channel_targets:
 - conda-forge main
 cxx_compiler:
 - clangxx
 cxx_compiler_version:
-- '12'
+- '14'
 hdf5:
-- 1.10.6
+- 1.12.2
 macos_machine:
 - x86_64-apple-darwin13.4.0
-macos_min_version:
-- '10.13'
 numpy:
 - '1.19'
 pin_run_as_build:
@@ -32,8 +30,6 @@ pin_run_as_build:
   python:
     min_pin: x.x
     max_pin: x.x
-  sqlite:
-    max_pin: x
 python:
 - 3.8.* *_cpython
 sqlite:
@@ -43,7 +39,7 @@ target_platform:
 zip_keys:
 - - c_compiler_version
   - cxx_compiler_version
-- - macos_min_version
-  - MACOSX_DEPLOYMENT_TARGET
 - - python
   - numpy
+zlib:
+- '1.2'

.circleci/config.yml

@@ -1,18 +1,18 @@
 # This file was generated automatically from conda-smithy. To update this configuration,
 # update the conda-forge.yml and/or the recipe/meta.yaml.
-# -*- mode: yaml -*-
+# -*- mode: jinja-yaml -*-
 
 version: 2
 
 jobs:
   build_linux_64_:
     working_directory: ~/test
     machine:
-      image: ubuntu-2004:current
+      - image: ubuntu-2004:current
     environment:
-      CONFIG: "linux_64_"
-      UPLOAD_PACKAGES: "False"
-      DOCKER_IMAGE: "quay.io/condaforge/linux-anvil-cos7-x86_64"
+      - CONFIG: "linux_64_"
+      - UPLOAD_PACKAGES: "False"
+        DOCKER_IMAGE: "quay.io/condaforge/linux-anvil-cos7-x86_64"
     steps:
       - checkout
       - run:
@@ -36,13 +36,4 @@ workflows:
   version: 2
   build_and_test:
     jobs:
-      - build_linux_64_:
-        # Knute says he only wants it to build for PR's
-        # That is accomplished by turning on "build only on pull requests"
-        # on https://app.circleci.com/settings/project/github/sparcians/map/advanced
-        # which still will build commits on master but we also add filters to ignore
-        # all branches here as suggested in https://discuss.circleci.com/t/only-build-pull-requests-not-every-branch/200/8
-          filters:
-            branches:
-              ignore: master
-
+      - build_linux_64_

.github/workflows/automerge.yml

@@ -0,0 +1,19 @@
+on:
+  status: {}
+  check_suite:
+    types:
+      - completed
+
+jobs:
+  automerge-action:
+    runs-on: ubuntu-latest
+    name: automerge
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+      - name: automerge-action
+        id: automerge-action
+        uses: conda-forge/automerge-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          rerendering_github_token: ${{ secrets.RERENDERING_GITHUB_TOKEN }}

.github/workflows/webservices.yml

@@ -0,0 +1,13 @@
+on: repository_dispatch
+
+jobs:
+  webservices:
+    runs-on: ubuntu-latest
+    name: webservices
+    steps:
+      - name: webservices
+        id: webservices
+        uses: conda-forge/webservices-dispatch-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          rerendering_github_token: ${{ secrets.RERENDERING_GITHUB_TOKEN }}

.scripts/build_steps.sh

@@ -24,15 +24,18 @@ export CONFIG_FILE="${CI_SUPPORT}/${CONFIG}.yaml"
 cat >~/.condarc <<CONDARC
 
 conda-build:
- root-dir: ${FEEDSTOCK_ROOT}/build_artifacts
+  root-dir: ${FEEDSTOCK_ROOT}/build_artifacts
+pkgs_dirs:
+  - ${FEEDSTOCK_ROOT}/build_artifacts/pkg_cache
+  - /opt/conda/pkgs
 
 CONDARC
 
 
 mamba install --update-specs --yes --quiet --channel conda-forge \
-    conda-build pip boa conda-forge-ci-setup=3
+    conda-build pip boa conda-forge-ci-setup=3 "py-lief<0.12"
 mamba update --update-specs --yes --quiet --channel conda-forge \
-    conda-build pip boa conda-forge-ci-setup=3
+    conda-build pip boa conda-forge-ci-setup=3 "py-lief<0.12"
 
 # set up the condarc
 setup_conda_rc "${FEEDSTOCK_ROOT}" "${RECIPE_ROOT}" "${CONFIG_FILE}"
@@ -46,6 +49,10 @@ make_build_number "${FEEDSTOCK_ROOT}" "${RECIPE_ROOT}" "${CONFIG_FILE}"
 
 ( endgroup "Configuring conda" ) 2> /dev/null
 
+if [[ -f "${FEEDSTOCK_ROOT}/LICENSE.txt" ]]; then
+  cp "${FEEDSTOCK_ROOT}/LICENSE.txt" "${RECIPE_ROOT}/recipe-scripts-license.txt"
+fi
+
 if [[ "${BUILD_WITH_CONDA_DEBUG:-0}" == 1 ]]; then
     if [[ "x${BUILD_OUTPUT_ID:-}" != "x" ]]; then
         EXTRA_CB_OPTIONS="${EXTRA_CB_OPTIONS:-} --output-id ${BUILD_OUTPUT_ID}"

.scripts/run_osx_build.sh

@@ -23,11 +23,10 @@ bash $MINIFORGE_FILE -b -p ${MINIFORGE_HOME}
 source ${MINIFORGE_HOME}/etc/profile.d/conda.sh
 conda activate base
 
-echo -e "\n\nInstalling ['conda-forge-ci-setup=3'] and conda-build."
 mamba install --update-specs --quiet --yes --channel conda-forge \
-    conda-build pip boa conda-forge-ci-setup=3
+    conda-build pip boa conda-forge-ci-setup=3 "py-lief<0.12"
 mamba update --update-specs --yes --quiet --channel conda-forge \
-    conda-build pip boa conda-forge-ci-setup=3
+    conda-build pip boa conda-forge-ci-setup=3 "py-lief<0.12"
 
 
 
@@ -57,6 +56,10 @@ echo -e "\n\nMaking the build clobber file"
 make_build_number ./ ./conda.recipe ./.ci_support/${CONFIG}.yaml
 
 
+if [[ -f LICENSE.txt ]]; then
+  cp LICENSE.txt "conda.recipe/recipe-scripts-license.txt"
+fi
+
 if [[ "${BUILD_WITH_CONDA_DEBUG:-0}" == 1 ]]; then
     if [[ "x${BUILD_OUTPUT_ID:-}" != "x" ]]; then
         EXTRA_CB_OPTIONS="${EXTRA_CB_OPTIONS:-} --output-id ${BUILD_OUTPUT_ID}"

README.md

@@ -20,3 +20,18 @@ MAP is broken into two parts:
 [![CircleCI](https://circleci.com/gh/sparcians/map.svg?style=svg)](https://circleci.com/gh/sparcians/map)
 [![MacOS Build Status](https://dev.azure.com/sparcians/map/_apis/build/status/sparcians.map?branchName=master&label=MacOS)](https://dev.azure.com/sparcians/map/_build/latest?definitionId=1&branchName=master)
 [![Documentation](https://github.com/sparcians/map/workflows/Documentation/badge.svg)](https://sparcians.github.io/map/)
+
+## Updating Regression/Build Environments
+
+CI files are generated when the command `conda smithy rerender` is run
+inside a MAP clone.  That command uses the following files to control
+the generation of the CI-specific control files:
+
+- `conda-forge.yml` - defines which platforms you want to support and some other higher-level things
+- `conda.recipe/conda_build_config.yaml` - defines lists of values for variables that are used in meta.yaml
+- `conda.recipe/meta.yaml` - uses variables (stuff inside {{ varname }} double curlies)
+
+To update versions of OSes, edit the following file:
+https://github.com/sparcians/map/blob/master/conda.recipe/conda_build_config.yaml
+and then run `conda smithy rerender`.  (Ensure `conda install
+conda-smithy` into your conda installation for that command to exist).

conda-forge.yml

@@ -8,8 +8,8 @@ skip_render:
   - build-locally.py
   - .github
 provider:
-  linux: circle
-  osx: azure
+  linux_64: circle
+  osx_64: azure
   win: None
   linux_ppc64le: None
   linux_aarch64: None

conda.recipe/conda_build_config.yaml

@@ -22,21 +22,13 @@
 # override macos APK min version.
 # conda-forge supports from 10.9 but we
 # have code that needs 10.13.
-# See https://sifive.atlassian.net/wiki/x/0IBBJw
-# for details
-macos_min_version:             # [osx]
-  - 10.13                      # [osx]
+macos_machine:                 # [osx]
+  - arm64-apple-darwin20.0.0   # [osx and arm64]
 MACOSX_DEPLOYMENT_TARGET:      # [osx]
-  - 10.13                      # [osx]
-
-zip_keys:                       # [osx]
-  -                             # [osx]
-    - macos_min_version         # [osx]
-    - MACOSX_DEPLOYMENT_TARGET  # [osx]
-
+  - 11.1                       # [osx]
 
 # linux_clang_version is not a part of zip_keys
-# from conda-forge, if you want to, you can 
+# from conda-forge, if you want to, you can
 # easily matrix the linux builds using the same
 # backend from gcc but adding new clang versions
 # here
@@ -94,7 +86,7 @@ python_impl:
 # cdt_name:
 #   - cos6
 #   - cos6
-# 
+#
 
 # conda-forge-pinnings-feedstock/recipe/conda_build_config.yaml
 # uses c_compiler_version and cxx_compiler_version in a zip_keys
@@ -111,7 +103,7 @@ python_impl:
 # list and keys can only be in one, so, we have to constrain fortran to be
 # a matrix as well even though we don't use it.
 #
-# If we really want to define our own zip_keys, we can rerender with 
+# If we really want to define our own zip_keys, we can rerender with
 # conda smithy rerender --exclusive-config <path to this file>
 #
 # and conda-smithy should just use our configuration
@@ -127,5 +119,3 @@ python_impl:
 #        - python
 #        - numpy
 #        - python_impl
-
-

conda.recipe/meta.yaml

@@ -57,6 +57,7 @@ requirements:
     - hdf5
     - python
     - rapidjson
+    - zlib
   run:
     - matplotlib-base
     - numpy

sparta/cmake/sparta-config.cmake

@@ -13,7 +13,7 @@
 ################################################################################
 
 # Find Boost
-set (_BOOST_COMPONENTS filesystem date_time iostreams serialization timer program_options)
+set (_BOOST_COMPONENTS date_time iostreams serialization timer program_options)
 if (COMPILE_WITH_PYTHON)
   list (APPEND _BOOST_COMPONENTS python)
   find_package (Python COMPONENTS Interpreter Development)
@@ -70,14 +70,19 @@ message (STATUS "Using RapidJSON CPP ${RapidJSON_VERSION}")
 find_package (SQLite3 3.19 REQUIRED)
 message (STATUS "Using SQLite3 ${SQLite3_VERSION}")
 
+# Find zlib
+find_package(ZLIB REQUIRED)
+message (STATUS "Using zlib ${ZLIB_VERSION_STRING}")
+include_directories(SYSTEM ${ZLIB_INCLUDE_DIRS})
+
 # Find HDF5. Need to enable C language for HDF5 testing
 enable_language (C)
 find_package (HDF5 1.10 REQUIRED)
 
 # Populate the Sparta_LIBS variable with the required libraries for
 # basic Sparta linking
-set (Sparta_LIBS sparta simdb ${HDF5_LIBRARIES} sqlite3 yaml-cpp z pthread
-  Boost::date_time Boost::filesystem Boost::iostreams Boost::serialization Boost::timer Boost::program_options)
+set (Sparta_LIBS sparta simdb ${HDF5_LIBRARIES} sqlite3 yaml-cpp ZLIB::ZLIB pthread
+  Boost::date_time Boost::iostreams Boost::serialization Boost::timer Boost::program_options)
 
 # On Linux we need to link against rt as well
 if (NOT APPLE)

sparta/doc/sparta_docs/building.txt

@@ -53,7 +53,6 @@
   z
   pthread
   Boost::date_time
-  Boost::filesystem
   Boost::iostreams
   Boost::serialization
   Boost::timer