Vendor kastore

.circleci/config.yml

@@ -3,17 +3,13 @@ version: 2.1
 commands:
   setup:
     steps:
-      - run:
-          name: Checkout submodules
-          command: |
-            git submodule update --init --recursive
       - run:
           name: Install dependencies and set path
           command: |
             sudo apt-get update
             sudo apt-get install -y ninja-build libcunit1-dev valgrind clang doxygen python3-pip
             # Install meson to the system packages so we can run it as root
-            sudo pip install meson==0.55
+            sudo pip install meson
             pip install numpy==1.18.5
             pip install --user -r python/requirements/CI-complete/requirements.txt
             pip install twine --user

.github/workflows/tests.yml

@@ -42,8 +42,6 @@ jobs:
 
       - name: Checkout
         uses: actions/checkout@v2
-        with:
-          submodules: true
 
       - name: Cache conda and dependancies
         id: cache
@@ -150,8 +148,6 @@ jobs:
 
     - name: 'Checkout'
       uses: actions/checkout@v2
-      with:
-        submodules: true
 
     - name: Setup MSYS2 ${{matrix.sys}}
       uses: msys2/setup-msys2@v2
@@ -165,12 +161,6 @@ jobs:
           mingw-w64-${{matrix.env}}-meson
           mingw-w64-${{matrix.env}}-cunit
 
-    - name: Fix windows symlinks
-      working-directory: c
-      run: |
-        rm -f subprojects/kastore
-        cp -r --dereference subprojects/full-projects/kastore/c subprojects/kastore
-
     - name: Build
       working-directory: c
       run: |

.github/workflows/wheels.yml

@@ -19,8 +19,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v2
-        with:
-            submodules: true
       - name: Set up Python ${{ matrix.python }}
         uses: actions/setup-python@v2
         with:
@@ -62,8 +60,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v2
-        with:
-            submodules: true
       - name: Install deps
         env:
           PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
@@ -110,8 +106,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v2
-        with:
-            submodules: true
 
       - name: Set up Python 3.8
         uses: actions/setup-python@v2

c/CHANGELOG.rst

@@ -30,6 +30,9 @@
   ``tsk_tree_t.interval.left`` and ``tsk_tree_t.interval.right`` respectively.
   (:user:`jeromekelleher`, :issue:`1686`, :pr:`1913`)
 
+- ``kastore`` is now vendored into this repo instead of being a git submodule. Developers need to run
+  ``git submodule update``. (:user:`jeromekelleher`, :issue:`1687`, :pr:`1973`)
+
 
 **Features**
 

c/meson.build

@@ -2,6 +2,7 @@ project('tskit', ['c', 'cpp'], default_options: ['c_std=c99', 'cpp_std=c++11'])
 
 kastore_proj = subproject('kastore')
 kastore_dep = kastore_proj.get_variable('kastore_dep')
+kastore_inc = kastore_proj.get_variable('kastore_inc')
 
 cc = meson.get_compiler('c')
 m_dep = cc.find_library('m', required: false)
@@ -22,10 +23,10 @@ lib_headers = [
     'tskit/genotypes.h', 'tskit/stats.h', 'tskit/convert.h', 'tskit/haplotype_matching.h']
 
 # Subprojects use the static library for simplicity.
-inc = include_directories(['.', 'tskit'])
+tskit_inc = [kastore_inc, include_directories(['.'])]
 tskit_lib = static_library('tskit',
     sources: lib_sources, dependencies: lib_deps)
-tskit_dep = declare_dependency(include_directories:inc, link_with: tskit_lib)
+tskit_dep = declare_dependency(include_directories:tskit_inc, link_with: tskit_lib)
 
 if not meson.is_subproject()
 

c/subprojects/kastore/README.md

@@ -0,0 +1,3 @@
+This directory is an abbreviated version of the kastore distribution source.
+
+All files should be updated when we are updating to a new kastore version.

c/subprojects/kastore/VERSION

@@ -0,0 +1 @@
+2.0.2