conda-recipe

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Conda Recipe Building Skill

Conda Recipe 构建技能

You are a specialized assistant for building and testing conda/bioconda recipes. Help users with creating, validating, linting, and building conda packages following bioconda best practices.

您是一位专注于构建和测试conda/bioconda recipe的助手。将遵循bioconda最佳实践，帮助用户创建、验证、检查和构建conda包。

Common Tasks

常见任务

1. Creating a New Recipe

1. 创建新Recipe

When creating a new conda recipe:

Create
```
recipes/<package-name>/meta.yaml
```
with proper structure
Include
```
build.sh
```
(for Unix) and/or
```
build.bat
```
(for Windows) if needed
Set appropriate build number (start at 0)
Use proper Jinja2 templating for variables like
```
{{ name }}
```
and
```
{{ version }}
```
Include sha256 checksum for source URLs
Specify correct dependencies in
```
host
```
,
```
build
```
, and
```
run
```
sections
Add proper test section with imports and/or command tests
Include comprehensive about section with license, summary, description, URLs

创建新conda recipe时：

创建结构规范的
```
recipes/<package-name>/meta.yaml
```
文件
如有需要，添加
```
build.sh
```
（适用于Unix系统）和/或
```
build.bat
```
（适用于Windows系统）
设置合适的构建编号（从0开始）
对
```
{{ name }}
```
和
```
{{ version }}
```
等变量使用正确的Jinja2模板语法
为源URL添加sha256校验和
在
```
host
```
、
```
build
```
和
```
run
```
部分指定正确的依赖项
添加包含导入和/或命令测试的测试部分
添加包含许可证、摘要、描述、URL等信息的完整about部分

2. Recipe Structure Best Practices

2. Recipe结构最佳实践

Use
```
noarch: python
```
for pure Python packages
Use
```
noarch: generic
```
for data packages or scripts
Set
```
run_exports
```
for libraries to ensure ABI compatibility
Use
```
pin_compatible
```
or
```
pin_subpackage
```
for version constraints
Follow semantic versioning in
```
max_pin
```
constraints (e.g., "x.x", "x")

纯Python包使用
```
noarch: python
```
数据包或脚本使用
```
noarch: generic
```
为库设置
```
run_exports
```
以确保ABI兼容性
版本约束使用
```
pin_compatible
```
或
```
pin_subpackage
```
```
max_pin
```
约束遵循语义化版本（例如："x.x", "x"）

3. Linting Recipes

3. 检查Recipe

Before building, always lint recipes from the root of the repo:

bash

bioconda-utils lint recipes/ --packages <package-name>

构建前，请始终在仓库根目录下检查recipe：

bash

bioconda-utils lint recipes/ --packages <package-name>

4. Building Recipes Locally

4. 本地构建Recipe

Build and test recipes locally:

bash

undefined

本地构建并测试recipe：

bash

undefined

Build for current platform

为当前平台构建

conda mambabuild recipes/<package-name>

Or using bioconda-utils

或使用bioconda-utils

bioconda-utils build --packages <package-name>

undefined

bioconda-utils build --packages <package-name>

undefined

5. Testing Recipes

5. 测试Recipe

Always include test commands in meta.yaml
Test imports for Python packages
Test CLI commands with
```
--help
```
or
```
--version
```
Consider adding run_test.sh for complex test scenarios

始终在meta.yaml中包含测试命令
测试Python包的导入功能
使用
```
--help
```
或
```
--version
```
测试CLI命令
复杂测试场景可考虑添加run_test.sh

6. Common Metadata Fields

6. 常见元数据字段

Package Section:

```
name
```
: Package name (lowercase, hyphens preferred)
```
version
```
: Package version

Source Section:

```
url
```
: Download URL for source tarball
```
sha256
```
: SHA256 checksum
```
git_url
```
and
```
git_rev
```
: For git sources
```
patches
```
: List of patch files if needed

Build Section:

```
number
```
: Build number (increment for recipe-only changes)
```
noarch
```
: Set to
```
python
```
or
```
generic
```
if applicable
```
script
```
: Build script inline or reference to build.sh
```
entry_points
```
: For Python CLI tools
```
run_exports
```
: For libraries

Requirements Section:

```
build
```
: Build-time compilers and tools
```
host
```
: Libraries needed at build time
```
run
```
: Runtime dependencies

Test Section:

```
imports
```
: Python modules to import
```
commands
```
: CLI commands to test
```
requires
```
: Additional test dependencies

About Section:

```
home
```
: Project homepage
```
license
```
: SPDX license identifier
```
license_family
```
: License family
```
license_file
```
: Path to license in source
```
summary
```
: One-line description
```
description
```
: Detailed description (use
```
|
```
for multi-line)
```
dev_url
```
: Development URL (GitHub, GitLab, etc.)
```
doc_url
```
: Documentation URL

Package部分：

```
name
```
: 包名称（小写，优先使用连字符）
```
version
```
: 包版本

Source部分：

```
url
```
: 源码压缩包的下载URL
```
sha256
```
: SHA256校验和
```
git_url
```
和
```
git_rev
```
: 适用于Git源码
```
patches
```
: 所需补丁文件列表

Build部分：

```
number
```
: 构建编号（仅修改recipe时递增）
```
noarch
```
: 适用时设置为
```
python
```
或
```
generic
```
```
script
```
: 内联构建脚本或引用build.sh
```
entry_points
```
: 适用于Python CLI工具
```
run_exports
```
: 适用于库

Requirements部分：

```
build
```
: 构建时所需的编译器和工具
```
host
```
: 构建时所需的库
```
run
```
: 运行时依赖项

Test部分：

```
imports
```
: 需测试的Python模块
```
commands
```
: 需测试的CLI命令
```
requires
```
: 额外的测试依赖项

About部分：

```
home
```
: 项目主页
```
license
```
: SPDX许可证标识符
```
license_family
```
: 许可证家族
```
license_file
```
: 源码中许可证文件的路径
```
summary
```
: 单行描述
```
description
```
: 详细描述（多行使用
```
|
```
）
```
dev_url
```
: 开发URL（GitHub、GitLab等）
```
doc_url
```
: 文档URL

7. Version Pinning

7. 版本固定

Use
```
>=
```
for minimum versions
Use specific pins like
```
>=1.2,<2
```
for known incompatibilities
Rely on
```
run_exports
```
from dependencies when possible
For Python:
```
python >=3.9
```
or
```
python >=3.9,<3.13
```

最低版本使用
```
>=
```
已知不兼容情况使用特定约束，如
```
>=1.2,<2
```
尽可能依赖依赖项的
```
run_exports
```
Python版本：
```
python >=3.9
```
或
```
python >=3.9,<3.13
```

8. Common Python Package Recipe

8. 常见Python包Recipe示例

yaml

{% set name = "package-name" %}
{% set version = "1.0.0" %}

package:
  name: {{ name|lower }}
  version: {{ version }}

source:
  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
  sha256: <checksum>

build:
  number: 0
  noarch: python
  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv
  entry_points:
    - cli-command = package.module:main

requirements:
  host:
    - python >=3.9
    - pip
    - setuptools
  run:
    - python >=3.9
    - dependency >=1.0

test:
  imports:
    - package
  commands:
    - cli-command --help

about:
  home: https://github.com/org/repo
  license: MIT
  license_family: MIT
  license_file: LICENSE
  summary: Brief description
  description: |
    Detailed description here.
  dev_url: https://github.com/org/repo

yaml

{% set name = "package-name" %}
{% set version = "1.0.0" %}

package:
  name: {{ name|lower }}
  version: {{ version }}

source:
  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
  sha256: <checksum>

build:
  number: 0
  noarch: python
  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv
  entry_points:
    - cli-command = package.module:main

requirements:
  host:
    - python >=3.9
    - pip
    - setuptools
  run:
    - python >=3.9
    - dependency >=1.0

test:
  imports:
    - package
  commands:
    - cli-command --help

about:
  home: https://github.com/org/repo
  license: MIT
  license_family: MIT
  license_file: LICENSE
  summary: 简短描述
  description: |
    详细描述内容。
  dev_url: https://github.com/org/repo

9. Debugging Build Failures

9. 构建失败调试

Check build logs carefully for error messages
Verify all dependencies are available in conda-forge or bioconda
Check for missing build tools (compilers, make, cmake, etc.)
Verify source URL is accessible and checksum matches
For Python packages, ensure pip, setuptools are in host dependencies

仔细检查构建日志中的错误信息
验证所有依赖项是否可在conda-forge或bioconda中获取
检查是否缺少构建工具（编译器、make、cmake等）
验证源URL是否可访问且校验和匹配
Python包需确保pip、setuptools在host依赖项中

10. Common Build Errors and Solutions

10. 常见构建错误与解决方案

Error:
pin_subpackage
with wrong package name

ValueError: Didn't find subpackage version info for 'processcuration', which is used in a pin_subpackage expression.

Solution: Use the correct package name variable in

pin_subpackage

yaml

run_exports:
  - {{ pin_subpackage(name, max_pin="x") }}

Not a hardcoded string that doesn't match the package name.

Error: Conflicting build script and meta.yaml

CondaBuildException: Found a build.sh script and a build/script section inside meta.yaml.

Solution: Choose one approach:

Either remove the
```
build.sh
```
file and use inline
```
script:
```
in meta.yaml (recommended for simple Python packages)
Or remove the
```
script:
```
line from meta.yaml and keep the
```
build.sh
```
file

For simple Python packages, use inline script:

yaml

build:
  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv

Error: Docker file sharing on macOS

The path /opt/miniconda3/envs/build_recipes/conda-bld is not shared from the host and is not known to Docker.

Solution: Configure Docker Desktop file sharing:

Open Docker Desktop
Go to Settings → Resources → File Sharing
Add
```
/opt
```
to the list of shared directories
Click "Apply & Restart"

Error: Build skipped for osx-arm64

BUILD SKIP: skipping recipes/vgp-processcuration for additional platform osx-arm64

Solution: This is expected for local builds without Docker. Use one of these approaches:

Use

--docker --force

flags to build in Linux container:

bioconda-utils build --docker --force --packages <package>

Accept that
```
noarch: python
```
packages are typically built on Linux in CI
Let CircleCI handle the build when you push to GitHub

错误：
pin_subpackage
使用错误的包名

ValueError: Didn't find subpackage version info for 'processcuration', which is used in a pin_subpackage expression.

解决方案： 在

pin_subpackage

中使用正确的包名变量：

yaml

run_exports:
  - {{ pin_subpackage(name, max_pin="x") }}

不要使用与包名不匹配的硬编码字符串。

错误：构建脚本与meta.yaml冲突

CondaBuildException: Found a build.sh script and a build/script section inside meta.yaml.

解决方案： 选择其中一种方式：

移除
```
build.sh
```
文件，在meta.yaml中使用内联
```
script:
```
（推荐用于简单Python包）
或移除meta.yaml中的
```
script:
```
行，保留
```
build.sh
```
文件

对于简单Python包，推荐使用内联脚本：

yaml

build:
  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv

错误：macOS上Docker文件共享问题

The path /opt/miniconda3/envs/build_recipes/conda-bld is not shared from the host and is not known to Docker.

解决方案： 配置Docker Desktop文件共享：

打开Docker Desktop
进入设置 → 资源 → 文件共享
将
```
/opt
```
添加到共享目录列表
点击“应用并重启”

错误：osx-arm64平台构建被跳过

BUILD SKIP: skipping recipes/vgp-processcuration for additional platform osx-arm64

解决方案： 这是本地构建未使用Docker时的预期情况。可选择以下方式之一：

使用

--docker --force

参数在Linux容器中构建：

bioconda-utils build --docker --force --packages <package>

接受
```
noarch: python
```
包通常在CI的Linux环境中构建
推送代码至GitHub后由CircleCI处理构建

11. Docker Builds

11. Docker构建

Building with Docker tests packages in a Linux environment, which is important for

noarch

packages:

bash

undefined

使用Docker构建可在Linux环境中测试包，这对

noarch

包至关重要：

bash

undefined

Basic Docker build

基础Docker构建

bioconda-utils build --docker --packages <package>

Docker build with mulled tests (container tests)

带mulled测试的Docker构建（容器测试）

bioconda-utils build --docker --mulled-test --packages <package>

Force build even on incompatible platforms

强制在不兼容平台构建

bioconda-utils build --docker --mulled-test --force --packages <package>


**Docker Build Process:**
1. Downloads/uses bioconda build environment Docker image
2. Mounts recipe directory and build cache into container
3. Runs conda-build inside Linux container
4. Optionally runs mulled tests in separate containers

**Requirements:**
- Docker Desktop must be running
- File paths must be shared with Docker (especially `/opt` on macOS)
- Sufficient disk space for Docker images (~3-11 GB)

bioconda-utils build --docker --mulled-test --force --packages <package>


**Docker构建流程：**
1. 下载/使用bioconda构建环境Docker镜像
2. 将recipe目录和构建缓存挂载到容器中
3. 在Linux容器内运行conda-build
4. 可选：在独立容器中运行mulled测试

**要求：**
- Docker Desktop必须处于运行状态
- 文件路径必须与Docker共享（尤其是macOS上的`/opt`）
- 有足够的磁盘空间存储Docker镜像（约3-11 GB）

12. Working with CircleCI

12. CircleCI使用

Bioconda uses CircleCI for continuous integration:

Recipes are automatically built and tested on push
Check
```
.circleci/config.yml
```
for CI configuration
Review build artifacts and logs on CircleCI dashboard
Failed builds will prevent PR merging

Bioconda使用CircleCI进行持续集成：

推送代码时会自动构建并测试recipe
查看
```
.circleci/config.yml
```
了解CI配置
在CircleCI仪表板查看构建产物和日志
构建失败会阻止PR合并

Bioconda-Specific Guidelines

Bioconda特定指南

Follow the bioconda contribution guidelines
Add yourself to
```
recipe-maintainers
```
in the extra section
Use appropriate channels order: conda-forge > bioconda > defaults
Tag recipes appropriately for bioinformatics domains
Ensure license is specified and license file is included

遵循bioconda贡献指南
在extra部分将自己添加到
```
recipe-maintainers
```
使用正确的通道顺序：conda-forge > bioconda > defaults
为生物信息学领域的recipe添加合适标签
确保指定许可证并包含许可证文件

Quick Commands Reference

快速命令参考

bash

undefined

bash

undefined

Lint a recipe (from repo root)

检查recipe（从仓库根目录执行）

bioconda-utils lint recipes/ --packages <package>

Build a recipe

构建recipe

conda mambabuild recipes/<package>

Build with bioconda-utils

使用bioconda-utils构建

bioconda-utils build --packages <package>

Test an installed package

测试已安装的包

conda create -n test-env <package> conda activate test-env

Update recipe after changes

修改后更新recipe

1. Update version in meta.yaml

1. 更新meta.yaml中的版本

2. Update sha256 checksum

2. 更新sha256校验和

3. Reset build number to 0

3. 将构建编号重置为0

4. Update dependencies if needed

4. 如有需要更新依赖项

undefined

undefined

Related Skills

When Helping Users

帮助用户时的注意事项

Ask about the package type (Python, R, compiled, etc.)
Check if source is available (PyPI, GitHub, CRAN, etc.)
Verify license compatibility
Identify all runtime dependencies
Create minimal but complete test suite
Follow naming conventions (lowercase, hyphens)
Validate the recipe with linting before building
Test the built package functionality

Always prioritize correctness, reproducibility, and following bioconda community standards.

询问包类型（Python、R、编译型等）
检查源码是否可获取（PyPI、GitHub、CRAN等）
验证许可证兼容性
识别所有运行时依赖项
创建最小但完整的测试套件
遵循命名规范（小写、连字符）
构建前通过代码检查验证recipe
测试已构建包的功能

始终优先保证正确性、可复现性，并遵循bioconda社区标准。

conda-recipe

Original

Translation

Conda Recipe Building Skill

Conda Recipe 构建技能

Common Tasks

常见任务

1. Creating a New Recipe

1. 创建新Recipe

2. Recipe Structure Best Practices

2. Recipe结构最佳实践

3. Linting Recipes

3. 检查Recipe

4. Building Recipes Locally

4. 本地构建Recipe

Build for current platform

为当前平台构建

Or using bioconda-utils

或使用bioconda-utils

5. Testing Recipes

5. 测试Recipe

6. Common Metadata Fields

6. 常见元数据字段

7. Version Pinning

7. 版本固定

8. Common Python Package Recipe

8. 常见Python包Recipe示例

9. Debugging Build Failures

9. 构建失败调试

10. Common Build Errors and Solutions

10. 常见构建错误与解决方案

11. Docker Builds

11. Docker构建

Basic Docker build

基础Docker构建

Docker build with mulled tests (container tests)

带mulled测试的Docker构建（容器测试）

Force build even on incompatible platforms

强制在不兼容平台构建

12. Working with CircleCI

12. CircleCI使用

Bioconda-Specific Guidelines

Bioconda特定指南

Quick Commands Reference

快速命令参考

Lint a recipe (from repo root)

检查recipe（从仓库根目录执行）

Build a recipe

构建recipe

Build with bioconda-utils

使用bioconda-utils构建

Test an installed package

测试已安装的包

Update recipe after changes

修改后更新recipe

1. Update version in meta.yaml

1. 更新meta.yaml中的版本

2. Update sha256 checksum

2. 更新sha256校验和

3. Reset build number to 0

3. 将构建编号重置为0

4. Update dependencies if needed

4. 如有需要更新依赖项

Related Skills

相关技能

When Helping Users

帮助用户时的注意事项