Rejiggle c deps

.circleci/config.yml

@@ -13,7 +13,7 @@ commands:
             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

@@ -71,11 +71,10 @@ jobs:
         working-directory: python
         if: matrix.os == 'windows-latest'
         run: |
-          rm -r lib
-          mkdir lib
-          cp -r --dereference ../c/subprojects lib/.
-          cp -r --dereference ../c/tskit lib/.
-          cp ../c/tskit.h lib/.
+          rm -r c-library
+          mkdir c-library
+          cp -r --dereference ../c/tskit c-library/
+          cp ../c/tskit.h c-library/
 
       - name: Fix windows .profile
         if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
@@ -165,12 +164,6 @@ 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

@@ -84,12 +84,11 @@ jobs:
           git reset --hard
           cd python
           ${PYTHON} -VV
-          # For some reason I can't work out the C compiler is not following symlinks
-          rm -r lib
-          mkdir lib
-          cp -r --dereference ../c/subprojects lib/.
-          cp -r --dereference ../c/tskit lib/.
-          cp ../c/tskit.h lib/.
+          # Fix symlinks for windows
+          rm -r c-library
+          mkdir c-library
+          cp -r --dereference ../c/tskit c-library/
+          cp ../c/tskit.h c-library/
           ${PYTHON} setup.py build_ext --inplace
       - name: Build Wheel
         env:

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "c/kastore"]
-	path = c/subprojects/full-projects/kastore
+	path = python/c-dependencies/kastore
 	url = https://github.com/tskit-dev/kastore.git

c/subprojects/kastore.wrap

@@ -0,0 +1,5 @@
+[wrap-file]
+directory = kastore-2.0.1
+source_url = https://github.com/tskit-dev/kastore/releases/download/C_2.0.1/kastore-2.0.1.tar.gz
+source_filename = kastore-2.0.1.tar.gz
+source_hash = eedd3af700f6adf2be01e2f2b768a167452edc35d0b468c9647b232864e9a65a

c/tests/meson-subproject/meson.build

@@ -1,5 +1,9 @@
 project('example', 'c')
 
+# TODO update this once we have the tskit wrap setup and can
+# test whether we can automatically pull in kastore or not.
+# https://github.com/tskit-dev/tskit/issues/1961
+
 kastore_proj = subproject('kastore')
 kastore_dep = kastore_proj.get_variable('kastore_dep')
 tskit_proj = subproject('tskit')

c/tests/meson-subproject/subprojects/kastore.wrap

@@ -0,0 +1 @@
+../../../subprojects/kastore.wrap

python/requirements/development.txt

@@ -10,8 +10,7 @@ h5py>=2.6.0
 jsonschema>=3.0.0
 jupyter-book>=0.12.1
 kastore
-# More recent meson is too strict. See #1515.
-meson<=0.56
+meson
 msgpack>=1.0.0
 msprime>=1.0.0
 networkx

python/requirements/development.yml

@@ -16,7 +16,7 @@ dependencies:
   - h5py>=2.6.0
   - jsonschema>=3.0.0
   - kastore
-  - meson<=0.56 # More recent meson is too strict. See #1515.
+  - meson
   - msprime>=1.0.0
   - networkx
   - ninja

python/setup.py

@@ -23,8 +23,8 @@ def finalize_options(self):
         self.include_dirs.append(numpy.get_include())
 
 
-libdir = "lib"
-kastore_dir = os.path.join(libdir, "subprojects", "kastore")
+libdir = "c-library"
+kastore_dir = os.path.join("c-dependencies", "kastore", "c")
 tsk_source_files = [
     "core.c",
     "tables.c",