Merge pull request #682 from jeromekelleher/tskit-1.0

jeromekelleher · web-flow · commit 2a06def51586 · 2022-06-27T15:19:29.000+01:00
Tskit 1.0
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -50,7 +50,8 @@ jobs:
       - run:
           name: Compile C with gcc
           command: |
-            CFLAGS=--coverage meson lib/ build-gcc && cd build-gcc && ninja
+            CFLAGS=--coverage meson lib/ build-gcc
+            ninja -C build-gcc
 
       - run:
           name: Compile C with clang
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -66,19 +66,6 @@ jobs:
           auto-update-conda: true
           use-only-tar-bz2: true
 
-      - name: Fix windows symlinks
-        working-directory: lib
-        if: matrix.os == 'windows-latest'
-        run: |
-          rm -r subprojects/kastore
-          rm -r subprojects/tskit
-          rm -r subprojects/git-submodules/tskit/c/subprojects
-          rm -r subprojects/git-submodules/tskit/c/tests
-          cp -r --dereference subprojects/git-submodules/kastore/c subprojects/kastore
-          cp -r --dereference subprojects/git-submodules/tskit/c subprojects/tskit
-          cp -r --dereference subprojects/git-submodules/tskit/python/lwt_interface/* subprojects/tskit/.
-          cp -r --dereference subprojects/git-submodules/tskit/python/lwt_interface ../lwt_interface
-
       - name: Fix windows .profile
         if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
         run: |
diff --git a/.gitmodules b/.gitmodules
@@ -1,6 +1,3 @@
-[submodule "lib/subprojects/git-submodules/kastore"]
-	path = lib/subprojects/git-submodules/kastore
-	url = https://github.com/tskit-dev/kastore.git
 [submodule "lib/subprojects/git-submodules/tskit"]
-	path = lib/subprojects/git-submodules/tskit
+	path = git-submodules/tskit
 	url = https://github.com/tskit-dev/tskit.git
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,7 +1,7 @@
 include lib/*.h
-include lib/subprojects/tskit/*.h
-include lib/subprojects/tskit/tskit/*.h
-include lib/subprojects/kastore/*.h
+include git-submodules/tskit/c/*.h
+include git-submodules/tskit/c/tskit/*.h
+include git-submodules/tskit/c/subprojects/kastore/*.h
 include README.txt
 include LICENSE
 recursive-include tests *.py
diff --git a/_tsinfermodule.c b/_tsinfermodule.c
@@ -50,9 +50,9 @@ handle_library_error(int err)
 }
 
 static int
-uint32_PyArray_converter(PyObject *in, PyObject **out)
+uint64_PyArray_converter(PyObject *in, PyObject **out)
 {
-    PyObject *ret = PyArray_FROMANY(in, NPY_UINT32, 1, 1, NPY_ARRAY_IN_ARRAY);
+    PyObject *ret = PyArray_FROMANY(in, NPY_UINT64, 1, 1, NPY_ARRAY_IN_ARRAY);
     if (ret == NULL) {
         return NPY_FAIL;
     }
@@ -439,7 +439,7 @@ TreeSequenceBuilder_init(TreeSequenceBuilder *self, PyObject *args, PyObject *kw
 
     self->tree_sequence_builder = NULL;
     if (!PyArg_ParseTupleAndKeywords(args, kwds, "O&|kk", kwlist,
-            uint32_PyArray_converter, &num_alleles,
+            uint64_PyArray_converter, &num_alleles,
             &max_nodes, &max_edges)) {
         goto out;
     }
diff --git a/git-submodules/tskit b/git-submodules/tskit
@@ -0,0 +1 @@
+Subproject commit 76b658163101c2d4c82843665e521e139b74d738
diff --git a/lib/meson.build b/lib/meson.build
@@ -1,7 +1,5 @@
 project('tsinfer', 'c')
-
-kastore_proj = subproject('kastore')
-kastore_dep = kastore_proj.get_variable('kastore_dep')
+ 
 tskit_proj = subproject('tskit')
 tskit_dep = tskit_proj.get_variable('tskit_dep')
 
@@ -22,10 +20,10 @@ tsinfer_sources =[
 
 avl_lib = static_library('avl', sources: ['avl.c'])
 tsinfer_lib = static_library('tsinfer', 
-    sources: tsinfer_sources, dependencies: [m_dep, kastore_dep, tskit_dep], 
+    sources: tsinfer_sources, dependencies: [m_dep, tskit_dep], 
     c_args: extra_c_args, link_with:[avl_lib])
 
 unit_tests = executable('tests', 
     sources: ['tests/tests.c'], 
-    link_with: [tsinfer_lib], dependencies:[cunit_dep, kastore_dep, tskit_dep])
+    link_with: [tsinfer_lib], dependencies:[cunit_dep, tskit_dep])
 test('Unit tests', unit_tests)
diff --git a/lib/subprojects/README b/lib/subprojects/README
@@ -0,0 +1,3 @@
+This wrapfile is just used by meson for compiling the C code for 
+tests. It's not used by the top-level Python module in any
+way - that uses a git submodule to get the tskit code.
diff --git a/lib/subprojects/git-submodules/kastore b/lib/subprojects/git-submodules/kastore
diff --git a/lib/subprojects/git-submodules/tskit b/lib/subprojects/git-submodules/tskit
diff --git a/lib/subprojects/kastore b/lib/subprojects/kastore
diff --git a/lib/subprojects/tskit b/lib/subprojects/tskit
diff --git a/lib/subprojects/tskit.wrap b/lib/subprojects/tskit.wrap
@@ -0,0 +1,6 @@
+[wrap-file]
+directory = tskit-1.0.0
+
+source_url = https://github.com/tskit-dev/tskit/releases/download/C_1.0.0/tskit-1.0.0.tar.xz
+source_filename = tskit-1.0.0.tar.xz
+source_hash = f8a085fc6ef170706b76a307e18be4ab425f31a1f50fa9765ab2c2d81eef65c2
diff --git a/lib/tests/tests.c b/lib/tests/tests.c
@@ -198,7 +198,7 @@ verify_round_trip(tsk_table_collection_t *tables, size_t num_samples, size_t num
     ret = tsk_table_collection_sort(tables, 0, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
-    ret = tsk_treeseq_init(&ts, tables, TSK_BUILD_INDEXES);
+    ret = tsk_treeseq_init(&ts, tables, TSK_TS_INIT_BUILD_INDEXES);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     /* tsk_treeseq_print_state(&ts, stdout); */
@@ -212,10 +212,10 @@ verify_round_trip(tsk_table_collection_t *tables, size_t num_samples, size_t num
         ret = tsk_vargen_next(&vargen, &var);
         /* printf("ret = %s\n", tsk_strerror(ret)); */
         CU_ASSERT_FATAL(ret >= 0);
-        CU_ASSERT_EQUAL(var->site->id, j);
-        CU_ASSERT_EQUAL(var->site->position, (double) j);
+        CU_ASSERT_EQUAL(var->site.id, j);
+        CU_ASSERT_EQUAL(var->site.position, (double) j);
         for (k = 0; k < num_samples; k++) {
-            CU_ASSERT_EQUAL(var->genotypes.i8[k], samples[k][j]);
+            CU_ASSERT_EQUAL(var->genotypes[k], samples[k][j]);
         }
     }
 
diff --git a/requirements/CI-tests-complete/requirements.txt b/requirements/CI-tests-complete/requirements.txt
@@ -6,7 +6,7 @@ h5py==3.6.0
 humanize==4.1.0
 lmdb==1.3.0
 matplotlib==3.4.1
-meson==0.56 # FIXME pinning meson for now, https://github.com/tskit-dev/tsinfer/issues/471
+meson==0.62.0 
 msprime==1.1.1
 numpy==1.21.6
 pandas==1.2.5
@@ -16,5 +16,5 @@ pytest-xdist==2.5.0
 seaborn==0.11.2
 sortedcontainers==2.4.0
 tqdm==4.64.0
-tskit==0.4.1
+tskit==0.5.0
 zarr==2.11.3
diff --git a/requirements/CI-tests-pip/requirements.txt b/requirements/CI-tests-pip/requirements.txt
@@ -10,5 +10,5 @@ pytest-xdist==2.5.0
 seaborn==0.11.2
 sortedcontainers==2.4.0
 tqdm==4.64.0
-tskit==0.4.1
+tskit==0.5.0
 zarr==2.11.3
diff --git a/setup.py b/setup.py
@@ -20,9 +20,9 @@ def finalize_options(self):
 
 
 libdir = "lib"
-tskroot = os.path.join(libdir, "subprojects", "tskit")
+tskroot = os.path.join("git-submodules", "tskit", "c")
 tskdir = os.path.join(tskroot, "tskit")
-kasdir = os.path.join(libdir, "subprojects", "kastore")
+kasdir = os.path.join(tskroot, "subprojects", "kastore")
 includes = [libdir, tskroot, tskdir, kasdir]
 
 tsi_source_files = [
@@ -81,7 +81,7 @@ def finalize_options(self):
         "tqdm",
         "humanize",
         "daiquiri",
-        "tskit>=0.3.7",
+        "tskit>=0.5.0",
         "numcodecs>=0.6",
         # issues 965 and 967 at zarr-python prevent usage of 2.11.0 and 2.11.1
         "zarr>=2.2,!=2.11.0,!=2.11.1,!=2.11.2",

Original file line number	Diff line number	Diff line change
`@@ -50,9 +50,9 @@ handle_library_error(int err)`
`50`	`50`	`}`
`51`	`51`
`52`	`52`	`static int`
`53`		`-uint32_PyArray_converter(PyObject in, PyObject *out)`
	`53`	`+uint64_PyArray_converter(PyObject in, PyObject *out)`
`54`	`54`	`{`
`55`		`- PyObject *ret = PyArray_FROMANY(in, NPY_UINT32, 1, 1, NPY_ARRAY_IN_ARRAY);`
	`55`	`+ PyObject *ret = PyArray_FROMANY(in, NPY_UINT64, 1, 1, NPY_ARRAY_IN_ARRAY);`
`56`	`56`	`if (ret == NULL) {`
`57`	`57`	`return NPY_FAIL;`
`58`	`58`	`}`
`@@ -439,7 +439,7 @@ TreeSequenceBuilder_init(TreeSequenceBuilder self, PyObject args, PyObject *kw`
`439`	`439`
`440`	`440`	`self->tree_sequence_builder = NULL;`
`441`	`441`	`if (!PyArg_ParseTupleAndKeywords(args, kwds, "O&\|kk", kwlist,`
`442`		`- uint32_PyArray_converter, &num_alleles,`
	`442`	`+ uint64_PyArray_converter, &num_alleles,`
`443`	`443`	`&max_nodes, &max_edges)) {`
`444`	`444`	`goto out;`
`445`	`445`	`}`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+This wrapfile is just used by meson for compiling the C code for`
	`2`	`+tests. It's not used by the top-level Python module in any`
	`3`	`+way - that uses a git submodule to get the tskit code.`