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clean up json handling #390

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merged 15 commits into from
Mar 6, 2024
Merged

clean up json handling #390

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e8d598d
Replace anonymous tuples in JSON parsing with structs.
macklin-10x Mar 1, 2024
57def9b
Invert data control flow in json reading.
macklin-10x Mar 1, 2024
8c21c0b
Finish cleaning up the JSON loading code.
macklin-10x Mar 1, 2024
082a674
unused var
macklin-10x Mar 1, 2024
ddad626
Finish refactoring JSON parsing to use the type we already have...
macklin-10x Mar 2, 2024
c9ea09e
Delete the manually-implemented JSON loading function.
macklin-10x Mar 2, 2024
f81ed7c
Replace lazy JSON reading with martian filetypes.
macklin-10x Mar 4, 2024
9ab8d96
Add syn to deny.toml.
macklin-10x Mar 5, 2024
245ca15
Allow martian-lang git repos.
macklin-10x Mar 5, 2024
ad13f63
Remove the not-needed manual de-escaping code.
macklin-10x Mar 5, 2024
bdd3439
Re-add missing chain_type setter.
macklin-10x Mar 5, 2024
4a35a0c
Load annotations as empty vec if missing.
macklin-10x Mar 6, 2024
a5cdba0
Load info as default if missing.
macklin-10x Mar 6, 2024
dcf69f9
Load filtered as default if missing.
macklin-10x Mar 6, 2024
644438b
Refactor JSON loading to avoid collecting into an intermediate vector.
macklin-10x Mar 6, 2024
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171 changes: 156 additions & 15 deletions Cargo.lock
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7 changes: 7 additions & 0 deletions deny.toml
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Expand Up @@ -130,6 +130,7 @@ allow-registry = ["https://github.com/rust-lang/crates.io-index"]
allow-git = [
# TODO: remove this
"https://github.com/Barandis/qd",
"https://github.com/martian-lang/martian-rust",
]

[sources.allow-org]
Expand All @@ -139,3 +140,9 @@ github = ["10XGenomics"]
gitlab = []
# 1 or more bitbucket.org organizations to allow git sources for
bitbucket = []


[[bans.skip]]
# many packages depend on syn 1
name = "syn"
version = "1.0.105"
2 changes: 2 additions & 0 deletions enclone_args/Cargo.toml
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Expand Up @@ -30,12 +30,14 @@ evalexpr = ">=7, <12"
expr_tools = { path = "../expr_tools" }
io_utils = { path = "../io_utils" }
itertools.workspace = true
martian-filetypes = { git = "https://github.com/martian-lang/martian-rust", branch = "master" }
rand = "0.8"
rayon = "1"
regex = { version = "1", default-features = false, features = ["std", "perf"] }
serde_json = "1"
string_utils = { path = "../string_utils" }
vdj_ann = { path = "../vdj_ann" }
vdj_types = { path = "../vdj_types" }
vector_utils = { path = "../vector_utils" }

[target.'cfg(not(windows))'.dependencies.hdf5]
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