Fix overall, especially Rust version, edition, and package version to…

… latest.

Cargo.toml

@@ -1,29 +1,29 @@
 [package]
 authors = ["DDBJ(Bioinformatics and DDBJ Center)"]
-edition = "2018"
-license = "Apache-2.0"
+edition = "2021"
+license = "apache-2.0"
 name = "yevis"
 readme = "https://github.com/sapporo-wes/yevis-cli/README.md"
 repository = "https://github.com/sapporo-wes/yevis-cli"
 version = "0.5.8"
 
 [dependencies]
-anyhow = {version = "1.0.58", features = ["backtrace"]}
-base64 = "0.13.0"
-chrono = {version = "0.4.19", features = ["serde"]}
-colored = "2.0.0"
+anyhow = {version = "1.0.79", features = ["backtrace"]}
+base64 = "0.21.7"
+chrono = {version = "0.4.33", features = ["serde"]}
+colored = "2.1.0"
 dotenv = "0.15.0"
-env_logger = "0.9.0"
-log = "0.4.17"
-regex = "1.5.6"
-reqwest = {version = "0.11.11", features = ["blocking", "json", "multipart"]}
+env_logger = "0.11.1"
+log = "0.4.20"
+regex = "1.10.3"
+reqwest = {version = "0.11.23", features = ["blocking", "json", "multipart"]}
 rust-crypto = "0.2.36"
-serde = {version = "1.0.137", features = ["derive"]}
-serde_json = "1.0.81"
-serde_with = "1.14.0"
-serde_yaml = "0.8.24"
-sha2 = "0.10.2"
+serde = {version = "1.0.196", features = ["derive"]}
+serde_json = "1.0.113"
+serde_with = "3.5.1"
+serde_yaml = "0.9.31"
+sha2 = "0.10.8"
 structopt = "0.3.26"
-tempfile = "3.3.0"
-url = {version = "2.2.2", features = ["serde"]}
-uuid = {version = "1.1.2", features = ["serde", "v4"]}
+tempfile = "3.9.0"
+url = {version = "2.5.0", features = ["serde"]}
+uuid = {version = "1.7.0", features = ["serde", "v4"]}

Dockerfile

@@ -14,7 +14,7 @@ RUN apt update && \
     apt clean && \
     rm -rf /var/lib/apt/lists/*
 
-RUN curl -fsSL -o /tmp/docker.tgz https://download.docker.com/linux/static/stable/$(uname -m)/docker-20.10.9.tgz && \
+RUN curl -fsSL -o /tmp/docker.tgz https://download.docker.com/linux/static/stable/$(uname -m)/docker-24.0.7.tgz && \
     tar -C /tmp -xf /tmp/docker.tgz && \
     mv /tmp/docker/* /usr/bin/ && \
     rm -rf /tmp/docker /tmp/docker.tgz
@@ -25,4 +25,4 @@ RUN chmod +x /usr/bin/yevis
 WORKDIR /app
 
 ENTRYPOINT ["yevis"]
-CMD [""]
+CMD [""]

Dockerfile-dev

@@ -1,4 +1,4 @@
-FROM rust:1.70-slim-bullseye
+FROM rust:1.75-slim-bullseye
 
 RUN apt update && \
     apt install -y --no-install-recommends \
@@ -10,7 +10,7 @@ RUN apt update && \
     apt clean && \
     rm -rf /var/lib/apt/lists/*
 
-RUN curl -fsSL -o /tmp/docker.tgz https://download.docker.com/linux/static/stable/$(uname -m)/docker-20.10.9.tgz && \
+RUN curl -fsSL -o /tmp/docker.tgz https://download.docker.com/linux/static/stable/$(uname -m)/docker-24.0.7.tgz && \
     tar -C /tmp -xf /tmp/docker.tgz && \
     mv /tmp/docker/* /usr/bin/ && \
     rm -rf /tmp/docker /tmp/docker.tgz
@@ -21,4 +21,4 @@ COPY . .
 ENV RUST_BACKTRACE=1
 
 ENTRYPOINT ["tini", "--"]
-CMD ["sleep", "infinity"]
+CMD ["sleep", "infinity"]

LICENSE

@@ -186,7 +186,7 @@ APPENDIX: How to apply the Apache License to your work.
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-Copyright 2021 DDBJ(Bioinformatics and DDBJ Center) t.ohta@nig.ac.jp
+Copyright 2021 DDBJ(Bioinformatics and DDBJ Center) tazro.ohta@chiba-u.jp
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

README.md

@@ -30,17 +30,17 @@ In addition, see the below links:
 Use a single binary that is built without any dependencies (supports Linux only):
 
 ```bash
-$ curl -fsSL -O https://github.com/sapporo-wes/yevis-cli/releases/latest/download/yevis
-$ chmod +x ./yevis
-$ ./yevis --help
+curl -fsSL -O https://github.com/sapporo-wes/yevis-cli/releases/latest/download/yevis
+chmod +x ./yevis
+./yevis --help
 ```
 
 Or, use the Docker environment:
 
 ```bash
-$ curl -O https://raw.githubusercontent.com/sapporo-wes/yevis-cli/main/docker-compose.yml
-$ docker compose up -d
-$ docker compose exec app yevis --help
+curl -O https://raw.githubusercontent.com/sapporo-wes/yevis-cli/main/compose.yml
+docker compose up -d
+docker compose exec app yevis --help
 ```
 
 ## Usage
@@ -311,7 +311,7 @@ See the GitHub Actions section for more details.
 
 #### Generated TRS Responses
 
-Please note, as raised in the issue https://github.com/ddbj/workflow-registry/issues/15 by @kinow, that the TRS responses generated by Yevis may not be fully compliant with the [TRS API](https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh/tool-registry-schemas/develop/openapi/openapi.yaml).
+Please note, as raised in the issue <https://github.com/ddbj/workflow-registry/issues/15> by @kinow, that the TRS responses generated by Yevis may not be fully compliant with the [TRS API](https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh/tool-registry-schemas/develop/openapi/openapi.yaml).
 
 To summarize the comments in this issue:
 
@@ -384,8 +384,8 @@ And the namespace is separated by the `version` as the TRS endpoint.
 Launch a development environment using `docker compose`:
 
 ```bash
-$ docker compose -f docker-compose.dev.yml up -d --build
-$ docker compose -f docker-compose.dev.yml exec app bash
+$ docker compose -f compose.dev.yml up -d --build
+$ docker compose -f compose.dev.yml exec app bash
 # cargo run -- --help
 yevis 0.4.0
 ...
@@ -427,7 +427,7 @@ libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f317b723000)
 Run unit tests:
 
 ```bash
-$ cargo test -- --test-threads=1 --nocapture
+cargo test -- --test-threads=1 --nocapture
 ```
 
 Several test workflows are prepared.
@@ -436,15 +436,15 @@ See [tests/README.md](https://github.com/sapporo-wes/yevis-cli/blob/main/tests/R
 ### Download artifacts from building GitHub Actions
 
 ```bash
-$ gh run --repo sapporo-wes/yevis-cli list --workflow build_binary --json databaseId --jq .[0].databaseId | xargs -I {} gh run --repo sapporo-wes/yevis-cli download {} -n yevis
+gh run --repo sapporo-wes/yevis-cli list --workflow build_binary --json databaseId --jq .[0].databaseId | xargs -I {} gh run --repo sapporo-wes/yevis-cli download {} -n yevis
 ```
 
 ### Release
 
 Use [`release.sh`](https://github.com/sapporo-wes/yevis-cli/blob/main/release.sh) as follows:
 
 ```bash
-$ bash release.sh <new_version>
+bash release.sh <new_version>
 ```
 
 ## License

docs/getting_started.md

@@ -92,7 +92,7 @@ Install [`yevis-cli`](https://github.com/sapporo-wes/yevis-cli), see [`yevis-cli
 In this document, uses a Docker environment since using M1 Mac (the binary is only built for Linux).
 
 ```bash=
-$ curl -fsSL -O https://raw.githubusercontent.com/sapporo-wes/yevis-cli/main/docker-compose.yml
+$ curl -fsSL -O https://raw.githubusercontent.com/sapporo-wes/yevis-cli/main/compose.yml
 $ docker compose up -d
 [+] Running 2/2
  ⠿ Network yevis-network  Created                                                                   0.0s
@@ -128,7 +128,7 @@ The generated `GitHub Personal Access Token` can be passed to `yevis-cli` in one
 This time, use environment variables:
 
 ```bash=
-$ export GITHUB_TOKEN=<PASTE_YOUR_TOKEN>
+export GITHUB_TOKEN=<PASTE_YOUR_TOKEN>
 ```
 
 #### 3.1.1. Describe metadata

docs/getting_started_ja.md

@@ -94,7 +94,7 @@ GitHub Pages の deploy アクションが完了すると、`yevis-web` が GitH
 このドキュメントでは、M1 Mac を使用しているため、Docker 環境を使用します （binary は Linux 用にのみビルドされています）。
 
 ```bash=
-$ curl -fsSL -O https://raw.githubusercontent.com/sapporo-wes/yevis-cli/main/docker-compose.yml
+$ curl -fsSL -O https://raw.githubusercontent.com/sapporo-wes/yevis-cli/main/compose.yml
 $ docker compose up -d
 [+] Running 2/2
  ⠿ Network yevis-network  Created                                                                   0.0s
@@ -130,7 +130,7 @@ DDBJ(Bioinformatics and DDBJ Center)
 今回は、環境変数を使用します。
 
 ```bash=
-$ export GITHUB_TOKEN=<PASTE_YOUR_TOKEN>
+export GITHUB_TOKEN=<PASTE_YOUR_TOKEN>
 ```
 
 #### 3.1.1. Describe metadata

release.sh

@@ -28,7 +28,7 @@ git merge develop
 
 echo "Rewrite files."
 sed -i "s/version=\"$PREV_VERSION\"/version=\"$NEW_VERSION\"/g" Dockerfile
-sed -i "s/yevis-cli:$PREV_VERSION/yevis-cli:$NEW_VERSION/g" docker-compose.yml
+sed -i "s/yevis-cli:$PREV_VERSION/yevis-cli:$NEW_VERSION/g" compose.yml
 sed -i "s/version = \"$PREV_VERSION\"/version = \"$NEW_VERSION\"/g" Cargo.toml
 
 echo "Update dependencies listed in Cargo.lock."
@@ -37,7 +37,7 @@ cargo update -p yevis
 sleep 3
 
 echo "Commit and push."
-git add Dockerfile docker-compose.yml Cargo.toml Cargo.lock
+git add Dockerfile compose.yml Cargo.toml Cargo.lock
 git commit -m "Update version to $NEW_VERSION"
 git push origin main