Merge pull request #7 from stijndcl/fix/felix-suggestions

Apply suggestions by Felix and Rien

.github/workflows/rust.yml

@@ -19,7 +19,7 @@ jobs:
         id: cache
         with:
           shared-key: ${{ env.CACHE_KEY }}
-      - run: cd scripts/helper_scripts/new-parsers && cargo fetch
+      - run: cd scripts/helper_scripts/unipept-database-rs && cargo fetch
         if: ${{ !steps.cache.outputs.cache-hit }}
 
   build:
@@ -32,7 +32,7 @@ jobs:
       - uses: Swatinem/rust-cache@v2
         with:
           shared-key: ${{ env.CACHE_KEY }}
-      - run: cd scripts/helper_scripts/new-parsers && cargo build --release
+      - run: cd scripts/helper_scripts/unipept-database-rs && cargo build --release
 
   format:
     name: Check formatting
@@ -46,7 +46,7 @@ jobs:
       - uses: Swatinem/rust-cache@v2
         with:
           shared-key: ${{ env.CACHE_KEY }}
-      - run: cd scripts/helper_scripts/new-parsers && cargo fmt --all --check
+      - run: cd scripts/helper_scripts/unipept-database-rs && cargo fmt --all --check
 
   lint:
     name: Linting
@@ -66,4 +66,5 @@ jobs:
           reporter: 'github-pr-check'
           fail_on_error: true
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          workdir: scripts/helper_scripts/new-parsers
+          workdir: scripts/helper_scripts/unipept-database-rs
+

LICENSE

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2023 Universiteit Gent
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

scripts/helper_scripts/unipept-database-rs/Cargo.toml

@@ -0,0 +1,19 @@
+[package]
+name = "unipept_database"
+version = "0.1.0"
+edition = "2021"
+authors = ["[email protected]", "Stijn De Clercq", "Bart Mesuere", "Pieter Verschaffelt", "Tibo Vande Moortele"]
+categories = ["command-line-utilities", "parser-implementations", "science"]
+keywords = ["uniprot", "unipept", "metaproteomics"]
+readme = "README.md"
+repository = "https://github.com/unipept/unipept-database"
+homepage = "https://unipept.ugent.be/"
+license = "MIT"
+
+[dependencies]
+anyhow = "1.0.75"
+bit-vec = "0.6.3"
+chrono = "0.4.31"
+clap = { version = "4.4.6", features = ["derive"] }
+smartstring = { version = "1.0" }
+uniprot = "0.7.0"