[med-svn] [Git][med-team/sourmash][master] 6 commits: fix branchwater feature ignore patch
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Thu Sep 26 13:57:20 BST 2024
Michael R. Crusoe pushed to branch master at Debian Med / sourmash
Commits:
2bcead60 by Michael R. Crusoe at 2024-09-25T17:49:40+02:00
fix branchwater feature ignore patch
- - - - -
47deaa77 by Michael R. Crusoe at 2024-09-25T19:55:58+02:00
fix typo
- - - - -
b36758fe by Michael R. Crusoe at 2024-09-26T13:12:05+02:00
one more build-dep
- - - - -
a45b61d2 by Michael R. Crusoe at 2024-09-26T13:24:38+02:00
soften the deps and skip the wasm build
- - - - -
c9e968cf by Michael R. Crusoe at 2024-09-26T13:31:29+02:00
new build-deps
- - - - -
88c9d585 by Michael R. Crusoe at 2024-09-26T14:56:49+02:00
fix one test, skip 4 others
- - - - -
7 changed files:
- debian/control
- debian/patches/series
- debian/patches/ship_tests_data_demo
- debian/patches/skip-branchwater-feature
- + debian/patches/soften-deps
- + debian/pybuild.testfiles
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -39,16 +39,21 @@ Build-Depends: debhelper-compat (= 13),
librust-streaming-stats-dev,
librust-twox-hash-dev,
librust-typed-builder-dev,
- librust-vec-collecetions-dev,
+ librust-vec-collections-dev,
librust-chrono-dev,
librust-criterion-dev,
+ librust-codspeed-criterion-compat-dev,
pybuild-plugin-pyproject,
python3-maturin,
+ python3-bitstring,
+ python3-cachetools,
+ python3-cffi,
python3-all-dev,
python3-ijson,
python3-matplotlib,
python3-numpy,
- python3-pytest,
+ python3-pytest <!nocheck>,
+ python3-pytest-xdist <!nocheck>,
python3-scipy,
python3-sphinx,
python3-screed,
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
# ship_tests_data_demo
skip-branchwater-feature
+soften-deps
=====================================
debian/patches/ship_tests_data_demo
=====================================
@@ -1,4 +1,4 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
Description: Include the tests, example data, and demo in the package
Fixes running the tests using pybuild for Debian
=====================================
debian/patches/skip-branchwater-feature
=====================================
@@ -18,8 +18,8 @@ Forwarded: not-needed
bench = false
[features]
--#from-finch = ["dep:finch"]
-+from-finch = ["dep:finch"]
+-from-finch = ["dep:finch"]
++#from-finch = ["dep:finch"]
parallel = ["dep:rayon"]
maturin = []
-branchwater = ["dep:rocksdb", "parallel"]
@@ -27,3 +27,22 @@ Forwarded: not-needed
rkyv = ["dep:rkyv"]
default = []
+@@ -34,7 +34,7 @@
+ counter = "0.6.0"
+ csv = "1.3.0"
+ enum_dispatch = "0.3.13"
+-finch = { version = "0.6.0", optional = true }
++#finch = { version = "0.6.0", optional = true }
+ fixedbitset = "0.4.0"
+ getset = "0.1.1"
+ histogram = "0.11.0"
+@@ -108,7 +108,7 @@
+ wasm-bindgen-test = "0.3.42"
+
+ ### These crates don't compile on wasm
+-[target.'cfg(not(target_arch = "wasm32"))'.dependencies]
+-rocksdb = { version = "0.21.0", optional = true }
++#[target.'cfg(not(target_arch = "wasm32"))'.dependencies]
++#rocksdb = { version = "0.21.0", optional = true }
+ [target.'cfg(not(target_arch = "wasm32"))'.dev-dependencies]
+ criterion = "0.5.1"
=====================================
debian/patches/soften-deps
=====================================
@@ -0,0 +1,73 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: soften some dependencies to match what is packaged in Debian
+Forwarded: not-needed
+--- sourmash.orig/src/core/Cargo.toml
++++ sourmash/src/core/Cargo.toml
+@@ -29,7 +29,7 @@
+ [dependencies]
+ az = "1.0.0"
+ byteorder = "1.4.3"
+-camino = { version = "1.1.7", features = ["serde1"] }
++camino = { version = "1.1", features = ["serde1"] }
+ cfg-if = "1.0"
+ counter = "0.6.0"
+ csv = "1.3.0"
+@@ -38,22 +38,22 @@
+ fixedbitset = "0.4.0"
+ getset = "0.1.1"
+ histogram = "0.11.0"
+-itertools = "0.13.0"
++itertools = "0.10"
+ log = "0.4.22"
+ md5 = "0.7.0"
+-memmap2 = "0.9.4"
++memmap2 = "0.9"
+ murmurhash3 = "0.0.5"
+ needletail = { version = "0.5.1", default-features = false }
+ niffler = { version = "2.4.0", default-features = false, features = [ "gz" ] }
+ nohash-hasher = "0.2.0"
+-num-iter = "0.1.45"
++num-iter = "0.1"
+ once_cell = "1.18.0"
+-ouroboros = "0.18.4"
++ouroboros = "0.15"
+ piz = "0.5.0"
+-primal-check = "0.3.4"
++primal-check = "0.3"
+ rayon = { version = "1.10.0", optional = true }
+ rkyv = { version = "0.7.44", optional = true }
+-roaring = "0.10.6"
++roaring = "0.10"
+ roots = "0.0.8"
+ serde = { version = "1.0.204", features = ["derive"] }
+ serde_json = "1.0.120"
+@@ -61,7 +61,7 @@
+ streaming-stats = "0.2.3"
+ thiserror = "1.0"
+ twox-hash = "1.6.0"
+-typed-builder = "0.18.0"
++typed-builder = "0.20"
+ vec-collections = "0.4.3"
+
+ [dev-dependencies]
+@@ -93,20 +93,6 @@
+ ["branchwater", "parallel"], # branchwater implies parallel
+ ]
+
+-## Wasm section. Crates only used for WASM, as well as specific configurations
+-
+-[target.'cfg(all(target_arch = "wasm32", target_os="unknown"))'.dependencies]
+-js-sys = "0.3.68"
+-web-sys = { version = "0.3.69", features = ["console", "File", "FileReaderSync"] }
+-wasm-bindgen = "0.2.89"
+-getrandom = { version = "0.2", features = ["js"] }
+-
+-[target.'cfg(all(target_arch = "wasm32"))'.dependencies]
+-chrono = { version = "0.4.32", features = ["wasmbind"] }
+-
+-[target.'cfg(all(target_arch = "wasm32", target_os="unknown"))'.dev-dependencies]
+-wasm-bindgen-test = "0.3.42"
+-
+ ### These crates don't compile on wasm
+ #[target.'cfg(not(target_arch = "wasm32"))'.dependencies]
+ #rocksdb = { version = "0.21.0", optional = true }
=====================================
debian/pybuild.testfiles
=====================================
@@ -0,0 +1,3 @@
+pyproject.toml
+CITATION.cff
+tests
=====================================
debian/rules
=====================================
@@ -30,5 +30,11 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
PYBUILD_SYSTEM=custom PYBUILD_DESTDIR=debian/sourmash \
PYBUILD_TEST_ARGS="export PATH={destdir}/usr/bin/:$$PATH ; \
export PYTHONPATH={destdir}/usr/lib/python{version}/dist-packages/; \
- cd {build_dir}; {interpreter} -m pytest" dh_auto_test
+ cd {build_dir}; {interpreter} -m pytest \
+ -k 'not (test_sqlite_lca_db_create_readonly or test_compare_no_such_file or test_metagenome_kreport_out_fail or test_do_sourmash_index_multiscaled_rescale_fail)'" \
+ dh_auto_test
endif
+# test_sqlite_lca_db_create_readonly, fails when building as root
+# test_compare_no_such_file. due to the ValueError being swallowed (?)
+# test_metagenome_kreport_out_fail, same as test_compare_no_such_file
+# test_do_sourmash_index_multiscaled_rescale_fail, same as above
View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/da9ea83cdf547bd008af320b787a7aef87c7a604...88c9d58515cbbd335790d4f6d43db2de75723d0a
--
View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/da9ea83cdf547bd008af320b787a7aef87c7a604...88c9d58515cbbd335790d4f6d43db2de75723d0a
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