Tidy up package and remove version from cargo.toml
This commit is contained in:
Tom
parent
4bcb09180e
commit
967adb1a69
4
.gitignore
vendored
4
.gitignore
vendored
@ -12,4 +12,6 @@ target/
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*.so
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_build/
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build/
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.ipynb_checkpoints/
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.ipynb_checkpoints/
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dist/
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Cargo.lock
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223
Cargo.lock
generated
223
Cargo.lock
generated
@ -1,223 +0,0 @@
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# This file is automatically @generated by Cargo.
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# It is not intended for manual editing.
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version = 4
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[[package]]
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name = "autocfg"
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||||
version = "1.4.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "ace50bade8e6234aa140d9a2f552bbee1db4d353f69b8217bc503490fc1a9f26"
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[[package]]
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name = "cfg-if"
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version = "1.0.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
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||||
|
||||
[[package]]
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||||
name = "heck"
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||||
version = "0.5.0"
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||||
source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
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[[package]]
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name = "indoc"
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version = "2.0.5"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5"
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[[package]]
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name = "itoa"
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version = "1.0.14"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "d75a2a4b1b190afb6f5425f10f6a8f959d2ea0b9c2b1d79553551850539e4674"
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[[package]]
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name = "libc"
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version = "0.2.169"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "b5aba8db14291edd000dfcc4d620c7ebfb122c613afb886ca8803fa4e128a20a"
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[[package]]
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name = "memchr"
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version = "2.7.4"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
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[[package]]
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name = "memoffset"
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version = "0.9.1"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a"
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dependencies = [
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"autocfg",
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]
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[[package]]
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name = "once_cell"
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version = "1.20.3"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "945462a4b81e43c4e3ba96bd7b49d834c6f61198356aa858733bc4acf3cbe62e"
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[[package]]
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name = "portable-atomic"
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version = "1.10.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "280dc24453071f1b63954171985a0b0d30058d287960968b9b2aca264c8d4ee6"
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[[package]]
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name = "proc-macro2"
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version = "1.0.93"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "60946a68e5f9d28b0dc1c21bb8a97ee7d018a8b322fa57838ba31cc878e22d99"
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dependencies = [
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"unicode-ident",
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]
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[[package]]
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name = "pyo3"
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version = "0.23.4"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "57fe09249128b3173d092de9523eaa75136bf7ba85e0d69eca241c7939c933cc"
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dependencies = [
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"cfg-if",
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"indoc",
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"libc",
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"memoffset",
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"once_cell",
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"portable-atomic",
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"pyo3-build-config",
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"pyo3-ffi",
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"pyo3-macros",
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"unindent",
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]
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[[package]]
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name = "pyo3-build-config"
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version = "0.23.4"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "1cd3927b5a78757a0d71aa9dff669f903b1eb64b54142a9bd9f757f8fde65fd7"
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dependencies = [
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"once_cell",
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"target-lexicon",
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]
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[[package]]
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name = "pyo3-ffi"
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version = "0.23.4"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "dab6bb2102bd8f991e7749f130a70d05dd557613e39ed2deeee8e9ca0c4d548d"
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dependencies = [
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"libc",
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"pyo3-build-config",
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]
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[[package]]
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name = "pyo3-macros"
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version = "0.23.4"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "91871864b353fd5ffcb3f91f2f703a22a9797c91b9ab497b1acac7b07ae509c7"
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dependencies = [
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"proc-macro2",
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"pyo3-macros-backend",
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"quote",
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"syn",
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]
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[[package]]
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name = "pyo3-macros-backend"
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version = "0.23.4"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "43abc3b80bc20f3facd86cd3c60beed58c3e2aa26213f3cda368de39c60a27e4"
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dependencies = [
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"heck",
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"proc-macro2",
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"pyo3-build-config",
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"quote",
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"syn",
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]
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[[package]]
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name = "qubed"
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version = "0.1.2"
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dependencies = [
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"pyo3",
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"serde",
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"serde_json",
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]
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[[package]]
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name = "quote"
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version = "1.0.38"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "0e4dccaaaf89514f546c693ddc140f729f958c247918a13380cccc6078391acc"
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dependencies = [
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"proc-macro2",
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]
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[[package]]
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name = "ryu"
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version = "1.0.19"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "6ea1a2d0a644769cc99faa24c3ad26b379b786fe7c36fd3c546254801650e6dd"
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[[package]]
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name = "serde"
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version = "1.0.217"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "02fc4265df13d6fa1d00ecff087228cc0a2b5f3c0e87e258d8b94a156e984c70"
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dependencies = [
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"serde_derive",
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]
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[[package]]
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name = "serde_derive"
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version = "1.0.217"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "5a9bf7cf98d04a2b28aead066b7496853d4779c9cc183c440dbac457641e19a0"
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dependencies = [
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"proc-macro2",
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"quote",
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"syn",
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]
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[[package]]
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name = "serde_json"
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version = "1.0.138"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "d434192e7da787e94a6ea7e9670b26a036d0ca41e0b7efb2676dd32bae872949"
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dependencies = [
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"itoa",
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"memchr",
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"ryu",
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"serde",
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]
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[[package]]
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name = "syn"
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version = "2.0.98"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "36147f1a48ae0ec2b5b3bc5b537d267457555a10dc06f3dbc8cb11ba3006d3b1"
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dependencies = [
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"proc-macro2",
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"quote",
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"unicode-ident",
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]
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[[package]]
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name = "target-lexicon"
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version = "0.12.16"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1"
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[[package]]
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name = "unicode-ident"
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version = "1.0.16"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "a210d160f08b701c8721ba1c726c11662f877ea6b7094007e1ca9a1041945034"
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[[package]]
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name = "unindent"
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version = "0.2.3"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce"
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@ -1,6 +1,6 @@
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[package]
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name = "qubed"
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version = "0.1.2"
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# version = "0.1.5"
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edition = "2021"
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repository = "https://github.com/ecmwf/qubed"
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@ -1,6 +1,6 @@
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[build-system]
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requires = ["setuptools", "wheel"]
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build-backend = "setuptools.build_meta"
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requires = ["maturin>=1.0,<2.0"]
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build-backend = "maturin"
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[project]
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name = "qubed"
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@ -56,11 +56,12 @@ def convert(args):
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new_branch = Qube.from_datacube(datacube)
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q = (q | Qube.from_datacube(datacube))
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output = match args.output_format:
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case "text":
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str(q)
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case "html":
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q.html()
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# output = match args.output_format:
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# case "text":
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# str(q)
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# case "html":
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# q.html()
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output = "fw"
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with open(args.output, "w") as f:
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f.write(output)
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@ -1 +0,0 @@
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from .fdb_schema_parser import FDBSchema, FDBSchemaFile, KeySpec, Key
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@ -1,375 +0,0 @@
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import dataclasses
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import json
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from dataclasses import dataclass, field
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from typing import Any
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import pe
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from pe.actions import Pack
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from pe.operators import Class, Star
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from .fdb_types import FDB_type_to_implementation, FDBType
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@dataclass(frozen=True)
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class KeySpec:
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"""
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Represents the specification of a single key in an FDB schema file. For example in
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```
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[ class, expver, stream=lwda, date, time, domain?
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[ type=ofb/mfb/oai
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[ obsgroup, reportype ]]]
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```
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class, expver, type=ofdb/mfb/oai etc are the KeySpecs
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These can have additional information such as: flags like `domain?`, allowed values like `type=ofb/mfb/oai`
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or specify type information with `date: ClimateMonthly`
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"""
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key: str
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type: FDBType = field(default_factory=FDBType)
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flag: str | None = None
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values: tuple = field(default_factory=tuple)
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comment: str = ""
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def __repr__(self):
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repr = self.key
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if self.flag:
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repr += self.flag
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# if self.type:
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# repr += f":{self.type}"
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if self.values:
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repr += "=" + "/".join(self.values)
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return repr
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def matches(self, key, value):
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# Sanity check!
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if self.key != key:
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return False
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# Some keys have a set of allowed values type=ofb/mfb/oai
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if self.values:
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if value not in self.values:
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return False
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# Check the formatting of values like Time or Date
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if self.type and not self.type.validate(value):
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return False
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return True
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def is_optional(self):
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if self.flag is None:
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return False
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return "?" in self.flag
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def is_allable(self):
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if self.flag is None:
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return False
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return "*" in self.flag
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@dataclass(frozen=True)
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class Comment:
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"Represents a comment node in the schema"
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value: str
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@dataclass(frozen=True)
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class FDBSchemaTypeDef:
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"Mapping between FDB schema key names and FDB Schema Types, i.e expver is of type Expver"
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key: str
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type: str
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# This is the schema grammar written in PEG format
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fdb_schema = pe.compile(
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r"""
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FDB < Line+ EOF
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Line < Schema / Comment / TypeDef / empty
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||||
|
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# Comments
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Comment <- "#" ~non_eol*
|
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non_eol <- [\x09\x20-\x7F] / non_ascii
|
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non_ascii <- [\x80-\uD7FF\uE000-\U0010FFFF]
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||||
|
||||
# Default Type Definitions
|
||||
TypeDef < String ":" String ";"
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||||
|
||||
# Schemas are the main attraction
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# They're a tree of KeySpecs.
|
||||
Schema < "[" KeySpecs (","? Schema)* "]"
|
||||
|
||||
# KeySpecs can be just a name i.e expver
|
||||
# Can also have a type expver:int
|
||||
# Or a flag expver?
|
||||
# Or values expver=xxx
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||||
KeySpecs < KeySpec_ws ("," KeySpec_ws)*
|
||||
KeySpec_ws < KeySpec
|
||||
KeySpec <- key:String (flag:Flag)? (type:Type)? (values:Values)? ([ ]* comment:Comment)?
|
||||
Flag <- ~("?" / "-" / "*")
|
||||
Type <- ":" [ ]* String
|
||||
Values <- "=" Value ("/" Value)*
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||||
|
||||
# Low level stuff
|
||||
Value <- ~([-a-zA-Z0-9_]+)
|
||||
String <- ~([a-zA-Z0-9_]+)
|
||||
EOF <- !.
|
||||
empty <- ""
|
||||
""",
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||||
actions={
|
||||
"Schema": Pack(tuple),
|
||||
"KeySpec": KeySpec,
|
||||
"Values": Pack(tuple),
|
||||
"Comment": Comment,
|
||||
"TypeDef": FDBSchemaTypeDef,
|
||||
},
|
||||
ignore=Star(Class("\t\f\r\n ")),
|
||||
# flags=pe.DEBUG,
|
||||
)
|
||||
|
||||
|
||||
def post_process(entries):
|
||||
"Take the raw output from the PEG parser and split it into type definitions and schema entries."
|
||||
typedefs = {}
|
||||
schemas = []
|
||||
for entry in entries:
|
||||
match entry:
|
||||
case c if isinstance(c, Comment):
|
||||
pass
|
||||
case t if isinstance(t, FDBSchemaTypeDef):
|
||||
typedefs[t.key] = t.type
|
||||
case s if isinstance(s, tuple):
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||||
schemas.append(s)
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||||
case _:
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||||
raise ValueError
|
||||
return typedefs, tuple(schemas)
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||||
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||||
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||||
def determine_types(types, node):
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||||
"Recursively walk a schema tree and insert the type information."
|
||||
if isinstance(node, tuple):
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||||
return [determine_types(types, n) for n in node]
|
||||
return dataclasses.replace(node, type=types.get(node.key, FDBType()))
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||||
|
||||
|
||||
@dataclass
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||||
class Key:
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||||
key: str
|
||||
value: Any
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||||
key_spec: KeySpec
|
||||
reason: str
|
||||
|
||||
def str_value(self):
|
||||
return self.key_spec.type.format(self.value)
|
||||
|
||||
def __bool__(self):
|
||||
return self.reason in {"Matches", "Skipped", "Select All"}
|
||||
|
||||
def emoji(self):
|
||||
return {"Matches": "✅", "Skipped": "⏭️", "Select All": "★"}.get(
|
||||
self.reason, "❌"
|
||||
)
|
||||
|
||||
def info(self):
|
||||
return f"{self.emoji()} {self.key:<12}= {str(self.value):<12} ({self.key_spec}) {self.reason if not self else ''}"
|
||||
|
||||
def __repr__(self):
|
||||
return f"{self.key}={self.key_spec.type.format(self.value)}"
|
||||
|
||||
def as_json(self):
|
||||
return dict(
|
||||
key=self.key,
|
||||
value=self.str_value(),
|
||||
reason=self.reason,
|
||||
)
|
||||
|
||||
|
||||
class FDBSchema:
|
||||
"""
|
||||
Represents a parsed FDB Schema file.
|
||||
Has methods to validate and convert request dictionaries to a mars request form with validation and type information.
|
||||
"""
|
||||
|
||||
def __init__(self, string, defaults: dict[str, str] = {}):
|
||||
"""
|
||||
1. Use a PEG parser on a schema string,
|
||||
2. Separate the output into schemas and typedefs
|
||||
3. Insert any concrete implementations of types from fdb_types.py defaulting to generic string type
|
||||
4. Walk the schema tree and annotate it with type information.
|
||||
"""
|
||||
m = fdb_schema.match(string)
|
||||
g = list(m.groups())
|
||||
self._str_types, schemas = post_process(g)
|
||||
self.types = {
|
||||
key: FDB_type_to_implementation[type]
|
||||
for key, type in self._str_types.items()
|
||||
}
|
||||
self.schemas = determine_types(self.types, schemas)
|
||||
self.defaults = defaults
|
||||
|
||||
def __repr__(self):
|
||||
return json.dumps(
|
||||
dict(schemas=self.schemas, defaults=self.defaults), indent=4, default=repr
|
||||
)
|
||||
|
||||
@classmethod
|
||||
def consume_key(
|
||||
cls, key_spec: KeySpec, request: dict[str, Any]
|
||||
) -> Key:
|
||||
key = key_spec.key
|
||||
try:
|
||||
value = request[key]
|
||||
except KeyError:
|
||||
if key_spec.is_optional():
|
||||
return Key(key_spec.key, "", key_spec, "Skipped")
|
||||
if key_spec.is_allable():
|
||||
return Key(key_spec.key, "", key_spec, "Select All")
|
||||
else:
|
||||
return Key(
|
||||
key_spec.key, "", key_spec, "Key Missing"
|
||||
)
|
||||
|
||||
if key_spec.matches(key, value):
|
||||
return Key(
|
||||
key_spec.key,
|
||||
key_spec.type.parse(value),
|
||||
key_spec,
|
||||
"Matches",
|
||||
)
|
||||
else:
|
||||
return Key(
|
||||
key_spec.key, value, key_spec, "Incorrect Value"
|
||||
)
|
||||
|
||||
@classmethod
|
||||
def _DFS_match(
|
||||
cls, tree: list, request: dict[str, Any]
|
||||
) -> tuple[bool | list, list[Key]]:
|
||||
"""Do a DFS on the schema tree, returning the deepest matching path
|
||||
At each stage return whether we matched on this path, and the path itself.
|
||||
|
||||
When traversing the tree there are three cases to consider:
|
||||
1. base case []
|
||||
2. one schema [k, k, k, [k, k, k]]
|
||||
3. list of schemas [[k,k,k], [k,k,k], [k,k,k]]
|
||||
"""
|
||||
# Case 1: Base Case
|
||||
if not tree:
|
||||
return True, []
|
||||
|
||||
# Case 2: [k, k, k, [k, k, k]]
|
||||
if isinstance(tree[0], KeySpec):
|
||||
node, *tree = tree
|
||||
# Check if this node is in the request
|
||||
match_result = cls.consume_key(node, request)
|
||||
|
||||
# If if isn't then terminate this path here
|
||||
if not match_result:
|
||||
return False, [match_result,] # fmt: skip
|
||||
|
||||
# Otherwise continue walking the tree and return the best result
|
||||
matched, path = cls._DFS_match(tree, request)
|
||||
|
||||
# Don't put the key in the path if it's optional and we're skipping it.
|
||||
if match_result.reason != "Skipped":
|
||||
path = [match_result,] + path # fmt: skip
|
||||
|
||||
return matched, path
|
||||
|
||||
# Case 3: [[k, k, k], [k, k, k]]
|
||||
branches = []
|
||||
for branch in tree:
|
||||
matched, branch_path = cls._DFS_match(branch, request)
|
||||
|
||||
# If this branch matches, terminate the DFS and use this.
|
||||
if matched:
|
||||
return branch, branch_path
|
||||
else:
|
||||
branches.append(branch_path)
|
||||
|
||||
# If no branch matches, return the one with the deepest match
|
||||
return False, max(branches, key=len)
|
||||
|
||||
@classmethod
|
||||
def _DFS_match_all(
|
||||
cls, tree: list, request: dict[str, Any]
|
||||
) -> list[list[Key]]:
|
||||
"""Do a DFS on the schema tree, returning all matching paths or partial matches.
|
||||
At each stage return all matching paths and the deepest partial matches.
|
||||
|
||||
When traversing the tree there are three cases to consider:
|
||||
1. base case []
|
||||
2. one schema [k, k, k, [k, k, k]]
|
||||
3. list of schemas [[k,k,k], [k,k,k], [k,k,k]]
|
||||
"""
|
||||
# Case 1: Base Case
|
||||
if not tree:
|
||||
return [[]]
|
||||
|
||||
# Case 2: [k, k, k, [k, k, k]]
|
||||
if isinstance(tree[0], KeySpec):
|
||||
node, *tree = tree
|
||||
# Check if this node is in the request
|
||||
request_values = request.get(node.key, None)
|
||||
|
||||
if request_values is None:
|
||||
# If the key is not in the request, return a partial match with Key Missing
|
||||
return [[Key(node.key, "", node, "Key Missing")]]
|
||||
|
||||
# If the request value is a list, try to match each value
|
||||
if isinstance(request_values, list):
|
||||
all_matches = []
|
||||
for value in request_values:
|
||||
match_result = cls.consume_key(node, {node.key: value})
|
||||
|
||||
if match_result:
|
||||
sub_matches = cls._DFS_match_all(tree, request)
|
||||
for match in sub_matches:
|
||||
if match_result.reason != "Skipped":
|
||||
match.insert(0, match_result)
|
||||
all_matches.append(match)
|
||||
|
||||
return all_matches if all_matches else [[Key(node.key, "", node, "No Match Found")]]
|
||||
else:
|
||||
# Handle a single value
|
||||
match_result = cls.consume_key(node, request)
|
||||
|
||||
# If it isn't then return a partial match with Key Missing
|
||||
if not match_result:
|
||||
return [[Key(node.key, "", node, "Key Missing")]]
|
||||
|
||||
# Continue walking the tree and get all matches
|
||||
all_matches = cls._DFS_match_all(tree, request)
|
||||
|
||||
# Prepend the current match to all further matches
|
||||
for match in all_matches:
|
||||
if match_result.reason != "Skipped":
|
||||
match.insert(0, match_result)
|
||||
|
||||
return all_matches
|
||||
|
||||
# Case 3: [[k, k, k], [k, k, k]]
|
||||
all_branch_matches = []
|
||||
for branch in tree:
|
||||
branch_matches = cls._DFS_match_all(branch, request)
|
||||
all_branch_matches.extend(branch_matches)
|
||||
|
||||
# Return all of the deepest partial matches or complete matches
|
||||
return all_branch_matches
|
||||
|
||||
def match_all(self, request: dict[str, Any]):
|
||||
request = request | self.defaults
|
||||
return self._DFS_match_all(self.schemas, request)
|
||||
|
||||
def match(self, request: dict[str, Any]):
|
||||
request = request | self.defaults
|
||||
return self._DFS_match(self.schemas, request)
|
||||
|
||||
|
||||
class FDBSchemaFile(FDBSchema):
|
||||
def __init__(self, path: str):
|
||||
with open(path, "r") as f:
|
||||
return super().__init__(f.read())
|
||||
@ -1,83 +0,0 @@
|
||||
from dataclasses import dataclass
|
||||
from typing import Any
|
||||
import re
|
||||
from collections import defaultdict
|
||||
from datetime import datetime, date, time
|
||||
|
||||
|
||||
@dataclass(repr=False)
|
||||
class FDBType:
|
||||
"""
|
||||
Holds information about how to format and validate a given FDB Schema type like Time or Expver
|
||||
This base type represents a string and does no validation or formatting. It's the default type.
|
||||
"""
|
||||
|
||||
name: str = "String"
|
||||
|
||||
def __repr__(self) -> str:
|
||||
return self.name
|
||||
|
||||
def validate(self, s: Any) -> bool:
|
||||
try:
|
||||
self.parse(s)
|
||||
return True
|
||||
except (ValueError, AssertionError):
|
||||
return False
|
||||
|
||||
def format(self, s: Any) -> str:
|
||||
return str(s).lower()
|
||||
|
||||
def parse(self, s: str) -> Any:
|
||||
return s
|
||||
|
||||
|
||||
@dataclass(repr=False)
|
||||
class Expver_FDBType(FDBType):
|
||||
name: str = "Expver"
|
||||
|
||||
def parse(self, s: str) -> str:
|
||||
assert bool(re.match(".{4}", s))
|
||||
return s
|
||||
|
||||
|
||||
@dataclass(repr=False)
|
||||
class Time_FDBType(FDBType):
|
||||
name: str = "Time"
|
||||
time_format = "%H%M"
|
||||
|
||||
def format(self, t: time) -> str:
|
||||
return t.strftime(self.time_format)
|
||||
|
||||
def parse(self, s: datetime | str | int) -> time:
|
||||
if isinstance(s, str):
|
||||
assert len(s) == 4
|
||||
return datetime.strptime(s, self.time_format).time()
|
||||
if isinstance(s, datetime):
|
||||
return s.time()
|
||||
return self.parse(f"{s:04}")
|
||||
|
||||
|
||||
@dataclass(repr=False)
|
||||
class Date_FDBType(FDBType):
|
||||
name: str = "Date"
|
||||
date_format: str = "%Y%m%d"
|
||||
|
||||
def format(self, d: Any) -> str:
|
||||
if isinstance(d, date):
|
||||
return d.strftime(self.date_format)
|
||||
if isinstance(d, int):
|
||||
return f"{d:08}"
|
||||
else:
|
||||
return d
|
||||
|
||||
def parse(self, s: datetime | str | int) -> date:
|
||||
if isinstance(s, str):
|
||||
return datetime.strptime(s, self.date_format).date()
|
||||
elif isinstance(s, datetime):
|
||||
return s.date()
|
||||
return self.parse(f"{s:08}")
|
||||
|
||||
|
||||
FDB_type_to_implementation = defaultdict(lambda: FDBType()) | {
|
||||
cls.name: cls() for cls in [Expver_FDBType, Time_FDBType, Date_FDBType]
|
||||
}
|
||||
Loading…
x
Reference in New Issue
Block a user