Resurrect CI

Author: vmarkovtsev

Dockerfile

@@ -8,7 +8,7 @@ ENV BROWSER=/browser \
     PYTHON_TARGET_VERSION="3.11.0-1+jammy1" \
     PYTHON_VERSION=3.11 \
     MKL=2020.4-304 \
-    LLVM=17
+    LLVM=21
 
 RUN echo '#!/bin/bash\n\
 \n\
@@ -21,8 +21,7 @@ echo\n' > /browser && \
 RUN apt-get update && \
     apt-get install -y --no-install-suggests --no-install-recommends gnupg gcc ca-certificates wget && \
     echo "deb https://apt.repos.intel.com/mkl all main" > /etc/apt/sources.list.d/intel-mkl.list && \
-    wget -O - https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB | \
-    apt-key add - && \
+    apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys BAC6F0C353D04109 && \
     apt-get update && \
     apt-get install -y --no-install-suggests --no-install-recommends intel-mkl-common-c-$MKL intel-mkl-gnu-rt-$MKL intel-mkl-f95-$MKL && \
     rm -rf \
@@ -63,7 +62,7 @@ RUN echo 'deb-src http://archive.ubuntu.com/ubuntu/ jammy main restricted' >>/et
     echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
     locale-gen && \
     echo "deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy main" >>/etc/apt/sources.list.d/llvm.list && \
-    wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | apt-key add - && \
+    apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 15CF4D18AF4F7421 && \
     apt-get update && \
     apt-get install -y bolt-$LLVM llvm-$LLVM && \
     export LLVM_SYMBOLIZER_PATH=/usr/lib/llvm-$LLVM/bin/llvm-symbolizer && \

server/athenian/api/internal/features/github/check_run_metrics_accelerated.pyx

@@ -93,7 +93,7 @@ def calculate_interval_intersections(starts: np.ndarray,
 cdef void _calculate_interval_intersections(const uint64_t[:] intervals,
                                             const int64_t[:] borders,
                                             char time_offset,
-                                            uint64_t[:] intersections) nogil:
+                                            uint64_t[:] intersections) noexcept nogil:
     cdef:
         int64_t i, j, border_index, group_start, group_finish, ii_open, intersections_offset
         uint64_t item, index_mask, timestamp, previous_timestamp, delta
@@ -161,7 +161,7 @@ cdef void _mark_check_suite_types(
     const int64_t[:] check_suite_sizes,
     int64_t[:] type_marks,
     mi_heap_destroy_stl_allocator[int64_t] *alloc,
-) nogil:
+) noexcept nogil:
     cdef:
         int64_t pos = 0, local_pos, size, previous_name, current_name
         size_t j

server/athenian/api/internal/miners/github/dag_accelerated.pyx

@@ -435,7 +435,7 @@ cdef void _recalculate_vertices_and_edges(
     uint32_t[:] old_vertex_map,
     uint32_t[:] result_vertexes,
     uint32_t[:] result_edges,
-) nogil:
+) noexcept nogil:
     cdef:
         uint32_t j, left, offset = 0, pos = 0, list_size
         uint32_t old_edge_i = 0, new_edge_i = 0, size = len(result_vertexes) - 1, i
@@ -944,7 +944,7 @@ cdef void _toposort(
     bool heads_order_is_significant,
     int32_t[:] order,
     mi_heap_destroy_stl_allocator[char] &alloc,
-) nogil:
+) noexcept nogil:
     """Topological sort of `heads`. The order is reversed!"""
     cdef:
         optional[mi_vector[uint32_t]] boilerplate
@@ -1095,7 +1095,7 @@ def mark_dag_parents(
 @cython.wraparound(False)
 cdef void _copy_parents_to_array(const mi_vector[mi_vector[uint32_t]] *parents,
                                  uint32_t[:] output,
-                                 int64_t[:] splits) nogil:
+                                 int64_t[:] splits) noexcept nogil:
     cdef:
         size_t i, offset = 0
         const mi_vector[uint32_t] *vec
@@ -1205,7 +1205,7 @@ cdef void _extract_first_parents(const uint32_t[:] vertexes,
                                  const uint32_t[:] edges,
                                  const uint32_t[:] heads,
                                  long max_depth,
-                                 char[:] first_parents) nogil:
+                                 char[:] first_parents) noexcept nogil:
     cdef:
         uint32_t head
         long i, depth
@@ -1260,7 +1260,7 @@ cdef void _partition_dag(
     const uint32_t[:] heads,
     char[:] borders,
     mi_heap_destroy_stl_allocator[char] &alloc,
-) nogil:
+) noexcept nogil:
     cdef:
         optional[mi_vector[uint32_t]] boilerplate
         optional[mi_vector[char]] visited_alloc
@@ -1358,7 +1358,7 @@ cdef void _extract_pr_commits(
     const uint32_t[:] pr_merges,
     int8_t[:] left_vertexes_map,
     mi_vector[mi_vector[uint32_t]] &pr_commits,
-) nogil:
+) noexcept nogil:
     cdef:
         long i
         uint32_t first, last, v, j, edge, peek
@@ -1495,7 +1495,7 @@ cdef void _extract_independent_ownership(
     uint32_t[:] left_vertexes,
     uint32_t[:] left_edges,
     mi_vector[mi_vector[uint32_t]] *result,
-) nogil:
+) noexcept nogil:
     cdef:
         int64_t i, p
         uint32_t j, head, parent, count, peek, edge

server/athenian/api/models/sql_builders.pyx

@@ -191,7 +191,7 @@ cdef void _in_any_values_array_int64(
     int length,
     int alignment,
     char *output,
-) nogil:
+) noexcept nogil:
     cdef:
         int i, pos = 7, valstart
         lldiv_t qr
@@ -625,7 +625,7 @@ cdef void _in_int64(const char *data,
                     int stride,
                     int length,
                     int alignment,
-                    char *output) nogil:
+                    char *output) noexcept nogil:
     cdef:
         int i, pos = 0, valstart
         lldiv_t qr

server/athenian/api/native/mi_heap_destroy_stl_allocator.pxd

@@ -35,7 +35,6 @@ cdef extern from "mi_heap_destroy_stl_allocator.h" nogil:
 
     cdef cppclass mi_vector[T](vector[T]):
         mi_vector mi_vector[X](mi_heap_destroy_stl_allocator[X]&) except +
-        T& emplace_back(...) except +
         mi_heap_destroy_stl_allocator[T] get_allocator()
 
     cdef cppclass mi_string(string):
@@ -47,6 +46,7 @@ cdef inline mi_heap_destroy_stl_allocator[char] *mi_heap_allocator_from_capsule(
     return <mi_heap_destroy_stl_allocator[char] *> PyCapsule_GetPointer(obj, b"mi_heap_destroy_stl_allocator")
 
 
-cdef inline void _delete_mi_heap_allocator_in_capsule(obj):
+cdef inline void _delete_mi_heap_allocator_in_capsule(obj) noexcept:
     cdef mi_heap_destroy_stl_allocator[char] *alloc = mi_heap_allocator_from_capsule(obj)
-    del alloc
+    if alloc != NULL:
+        del alloc

server/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools!=60.6.0,!=64.0.0", "wheel", "Cython>=0.29.30", "numpy==1.23.4"]
+requires = ["setuptools==75.3.0", "wheel", "Cython==3.0.12", "numpy==1.26.4"]
 
 [tool.pytest.ini_options]
 asyncio_mode = "auto"

server/requirements.txt

@@ -9,10 +9,10 @@ morcilla[sqlite,postgresql]==0.5.37
 psycopg2-binary==2.9.6
 xxhash==3.2.0
 # remember to change these versions in Dockerfile and pyproject.toml, too!
-numpy==1.23.4
+numpy==1.26.4
 # end of remember to change in Dockerfile
 scipy==1.10.1
-medvedi==0.1.67
+medvedi==0.1.68
 pytz==2023.3
 sentry-sdk[pure_eval]==1.19.1
 prometheus_client==0.14.1
@@ -44,7 +44,7 @@ psutil==5.9.4
 flogging==0.0.21
 unidecode==1.3.6
 pluralizer==1.2.0
-pyarrow==11.0.0
+pyarrow==14.0.2
 email-validator==1.3.1
 aiomonitor==0.4.5
 gunicorn==20.1.0