diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 8d8e23ce49..2ad9e7df51 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -12,6 +12,7 @@ updates: allow: - dependency-type: "direct" open-pull-requests-limit: 10 + rebase-strategy: "disabled" - package-ecosystem: "github-actions" directory: "/" schedule: diff --git a/.readthedocs.yml b/.readthedocs.yml index 0c7ae9f116..4a6db7b557 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -12,6 +12,10 @@ conda: environment: doc/environment.yml python: + # NOTE: doc/environment.yml specifies python=3.10, which is needed + # b/c of a pip problem; see + # https://github.com/sourmash-bio/sourmash/issues/2139 + # this 'version' setting is effectively ignored, AFAICT. -- CTB 7/24/22 version: 3.8 install: - method: pip diff --git a/Cargo.lock b/Cargo.lock index 576e2ce0bb..e094cd4bbf 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -140,6 +140,12 @@ dependencies = [ "rustc_version", ] +[[package]] +name = "cast" +version = "0.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5" + [[package]] name = "cc" version = "1.0.73" @@ -197,9 +203,9 @@ dependencies = [ [[package]] name = "counter" -version = "0.5.5" +version = "0.5.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "63b05d7acd00b53d97b7369c4062027ff55711db0c509f5b28d6d964a2f1ff87" +checksum = "48388d8711a360319610960332b6a6f9fc2b5a63bba9fd10f1b7aa50677d956f" dependencies = [ "num-traits", ] @@ -215,12 +221,12 @@ dependencies = [ [[package]] name = "criterion" -version = "0.3.5" +version = "0.3.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1604dafd25fba2fe2d5895a9da139f8dc9b319a5fe5354ca137cbbce4e178d10" +checksum = "b01d6de93b2b6c65e17c634a26653a29d107b3c98c607c765bf38d041531cd8f" dependencies = [ "atty", - "cast", + "cast 0.3.0", "clap", "criterion-plot", "csv", @@ -245,7 +251,7 @@ version = "0.4.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d00996de9f2f7559f7f4dc286073197f83e92256a59ed395f9aac01fe717da57" dependencies = [ - "cast", + "cast 0.2.7", "itertools", ] @@ -350,9 +356,9 @@ dependencies = [ [[package]] name = "fixedbitset" -version = "0.4.1" +version = "0.4.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "279fb028e20b3c4c320317955b77c5e0c9701f05a1d309905d6fc702cdc5053e" +checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80" [[package]] name = "flate2" @@ -510,9 +516,9 @@ dependencies = [ [[package]] name = "memmap2" -version = "0.5.4" +version = "0.5.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d5172b50c23043ff43dd53e51392f36519d9b35a8f3a410d30ece5d1aedd58ae" +checksum = "3a79b39c93a7a5a27eeaf9a23b5ff43f1b9e0ad6b1cdd441140ae53c35613fc7" dependencies = [ "libc", ] @@ -637,9 +643,9 @@ dependencies = [ [[package]] name = "once_cell" -version = "1.12.0" +version = "1.13.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7709cef83f0c1f58f666e746a08b21e0085f7440fa6a29cc194d68aac97a4225" +checksum = "18a6dbe30758c9f83eb00cbea4ac95966305f5a7772f3f42ebfc7fc7eddbd8e1" [[package]] name = "oorandom" @@ -958,9 +964,9 @@ checksum = "a4a3381e03edd24287172047536f20cabde766e2cd3e65e6b00fb3af51c4f38d" [[package]] name = "serde" -version = "1.0.137" +version = "1.0.140" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "61ea8d54c77f8315140a05f4c7237403bf38b72704d031543aa1d16abbf517d1" +checksum = "fc855a42c7967b7c369eb5860f7164ef1f6f81c20c7cc1141f2a604e18723b03" dependencies = [ "serde_derive", ] @@ -977,9 +983,9 @@ dependencies = [ [[package]] name = "serde_derive" -version = "1.0.137" +version = "1.0.140" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1f26faba0c3959972377d3b2d306ee9f71faee9714294e41bb777f83f88578be" +checksum = "6f2122636b9fe3b81f1cb25099fcf2d3f542cdb1d45940d56c713158884a05da" dependencies = [ "proc-macro2", "quote", @@ -988,9 +994,9 @@ dependencies = [ [[package]] name = "serde_json" -version = "1.0.81" +version = "1.0.82" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9b7ce2b32a1aed03c558dc61a5cd328f15aff2dbc17daad8fb8af04d2100e15c" +checksum = "82c2c1fdcd807d1098552c5b9a36e425e42e9fbd7c6a37a8425f390f781f7fa7" dependencies = [ "itoa 1.0.1", "ryu", diff --git a/doc/environment.yml b/doc/environment.yml index f3840b2dce..129ee5700e 100644 --- a/doc/environment.yml +++ b/doc/environment.yml @@ -3,4 +3,5 @@ channels: - defaults dependencies: - rust - - python =3.8 + - python=3.10 + - pip diff --git a/flake.lock b/flake.lock index ad92340781..521c13d12e 100644 --- a/flake.lock +++ b/flake.lock @@ -64,11 +64,11 @@ }, "nixpkgs": { "locked": { - "lastModified": 1655481042, - "narHash": "sha256-XHbcywq2vIQ5CeH1OK3TN793jkiNAAZsSctS1PFgseo=", + "lastModified": 1658549974, + "narHash": "sha256-+D1gH6ecI14xDuObG07cd9XXhLDdLMRwOBDQmJcVluc=", "owner": "NixOS", "repo": "nixpkgs", - "rev": "103a4c0ae46afa9cf008c30744175315ca38e9f9", + "rev": "52dd719bbd13d9f0974e5c3c29c74aa249e5b091", "type": "github" }, "original": { @@ -150,11 +150,11 @@ ] }, "locked": { - "lastModified": 1655520266, - "narHash": "sha256-YEo20XNDKwFSMzg4wGDz/uxNmd/FleUPgVkFyWx3UWA=", + "lastModified": 1658544517, + "narHash": "sha256-ipu69vA0a6AcWZqnHLzeRhvnVZbURXALHLIsqQWtJe4=", "owner": "oxalica", "repo": "rust-overlay", - "rev": "da04f39d50ad2844e97a44015048c2510ca06c2f", + "rev": "4bd340885e39e0625fc6dda8a5a9d13c921ebb96", "type": "github" }, "original": { @@ -165,11 +165,11 @@ }, "utils": { "locked": { - "lastModified": 1653893745, - "narHash": "sha256-0jntwV3Z8//YwuOjzhV2sgJJPt+HY6KhU7VZUL0fKZQ=", + "lastModified": 1656928814, + "narHash": "sha256-RIFfgBuKz6Hp89yRr7+NR5tzIAbn52h8vT6vXkYjZoM=", "owner": "numtide", "repo": "flake-utils", - "rev": "1ed9fb1935d260de5fe1c2f7ee0ebaae17ed2fa1", + "rev": "7e2a3b3dfd9af950a856d66b0a7d01e3c18aa249", "type": "github" }, "original": { diff --git a/flake.nix b/flake.nix index cfef19b8c4..db03a85b04 100644 --- a/flake.nix +++ b/flake.nix @@ -68,7 +68,7 @@ sourmash = mach-nix-wrapper.buildPythonPackage { src = ./.; pname = "sourmash"; - version = "4.4.0"; + version = "4.4.2"; requirements = '' screed>=1.0.5 cffi>=1.14.0 @@ -80,11 +80,12 @@ bitstring<4,>=3.1.9 ''; requirementsExtra = '' - setuptools + setuptools >= 61 milksnake setuptools_scm[toml] >= 4, <6 + wheel >= 0.29.0 ''; - SETUPTOOLS_SCM_PRETEND_VERSION = "4.4.0"; + SETUPTOOLS_SCM_PRETEND_VERSION = "4.4.2"; DYLD_LIBRARY_PATH = "${self.packages.${system}.lib}/lib"; NO_BUILD = "1"; };