first commit

.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.pyc
+*.py[cod]
+*$py.class
+
+# C extensions
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+
+# Distribution / packaging
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+.installed.cfg
+*.egg
+MANIFEST
+
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+#  Usually these files are written by a python script from a template
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+
+# pyenv
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+
+# pipenv
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+
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+#   commonly ignored for libraries.
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+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
\ No newline at end of file

README.md

+**astropy 需升级至 5.3**  
+**老写法同时兼容本地nas和云上s3，只要读写路径以s3:// 协议开头会自动识别**  
+
+如果需要读写S3时，需要传入s3的密钥和endpoint等配置，有两种方法可选
+
+### 方法1 环境变量
+执行下面三个环境变量，本文档下面介绍到的所有方法都会尝试读取环境变量以获取配置
+```python
+s3_options = {
+    'key': os.getenv('S3_KEY'),
+    'secret': os.getenv('S3_SECRET'),
+    'endpoint_url': os.getenv('S3_ENDPOINT_URL')
+}
+```
+
+### 方法2 每次调用方法时传入 s3_options
+```
+在第一个kwargs参数位置指定s3_options, s3_options示例：
+```json
+s3_options = {
+    "key": "minioadmin", 
+    "secret": "minioadmin", 
+    "endpoint_url": "http://localhost:9000"
+}
+
+```
+## 本地到s3的上传与下载
+### 上传
+ ```python
+from csst_fs import s3_fs
+# single file，s3_options from env
+s3_fs.put('requirements.txt', 's3://csst-prod/gaia/test/requirements.txt')
+# single file，s3_options from function parameter
+s3_fs.put('requirements.txt', 's3://csst-prod/gaia/test/requirements.txt', s3_options=s3_options)
+# folder，to s3 s3://csst-prod/common
+s3_fs.put('./common', 's3://csst-prod/', recursive=True)
+s3_fs.put('./common', 's3://csst-prod/', s3_options=s3_options, recursive=True)
+
+```
+
+### 下载
+```python
+from csst_fs import s3_fs
+# single file
+s3_fs.get('s3://csst-prod/gaia/test/requirements.txt', 'requirements.txt')
+s3_fs.get('s3://csst-prod/gaia/test/requirements.txt', 'requirements.txt', s3_options=s3_options)
+# folder
+s3_fs.get('s3://csst-prod/gaia/data', './', recursive=True)
+s3_fs.get('s3://csst-prod/gaia/data', './', s3_options=s3_options, recursive=True)
+```
+
+## astropy直接读写s3的写法适配
+### fits.open
+#### 老写法
+```python
+fits.open(path)
+```
+usage reference:  
+[https://docs.astropy.org/en/stable/io/fits/api/files.html#open](https://docs.astropy.org/en/stable/io/fits/api/files.html#open)  
+#### 新写法
+ ```python
+from csst_fs import fsspec_fits
+fsspec_fits.open("s3://csst-prod/gaia/xx.fits")
+fsspec_fits.open("s3://csst-prod/gaia/xx.fits", s3_options=s3_options)
+```
+
+ ### fits.getheader
+ #### 老写法
+ ```python
+fits.getheader(filename=in_image_path, ext=1)
+```
+usage reference:
+[https://docs.astropy.org/en/stable/io/fits/api/files.html#getheader](https://docs.astropy.org/en/stable/io/fits/api/files.html#getheader)  
+
+#### 新写法
+```python
+from csst_fs import fsspec_fits
+fsspec_fits.getheader(filename=in_image_path, ext=1)
+fsspec_fits.getheader(filename=in_image_path, ext=1, s3_options=s3_options)
+```
+
+
+### fits.getdata
+#### 老写法
+ ```python
+fits.getdata(in_ref_flat)
+fits.getdata( in_ref_shutter, 1)
+```
+usage reference:
+[https://docs.astropy.org/en/stable/io/fits/api/files.html#getdata](https://docs.astropy.org/en/stable/io/fits/api/files.html#getdata)  
+
+#### 新写法
+```python
+from csst_fs import fsspec_fits
+fsspec_fits.getdata(in_ref_flat)
+fsspec_fits.getdata(in_ref_flat, s3_options=s3_options)
+fsspec_fits.getdata( in_ref_shutter, 1)
+fsspec_fits.getdata( in_ref_shutter, 1, s3_options=s3_options)
+```
+
+### header.tofile
+#### 老写法
+```python
+header.tofile(out_head_path)
+```
+usage reference:
+[https://docs.astropy.org/en/stable/io/fits/api/headers.html#astropy.io.fits.Header.tofile](https://docs.astropy.org/en/stable/io/fits/api/headers.html#astropy.io.fits.Header.tofile)  
+
+#### 新写法
+```python
+from csst_fs import fsspec_header
+fsspec_header.tofile(header, out_head_path)
+fsspec_header.tofile(header, out_head_path, s3_options=s3_options)
+```
+
+
+ ### header.fromfile
+ #### 老写法
+ ```python
+header.fromfile(filename)
+```
+usage reference:
+[https://docs.astropy.org/en/stable/io/fits/api/headers.html#astropy.io.fits.Header.fromfile](https://docs.astropy.org/en/stable/io/fits/api/headers.html#astropy.io.fits.Header.fromfile)  
+
+#### 新写法
+```python
+from csst_fs import fsspec_header
+fsspec_header.fromfile(filename)
+fsspec_header.fromfile(filename, s3_options=s3_options)
+```
+
+
+### HDUList.writeto
+#### 老写法
+```python
+hdul_img.writeto(hdul_img, out_combined_img, overwrite=True)
+```
+usage reference:
+[https://docs.astropy.org/en/stable/io/fits/api/hdulists.html#astropy.io.fits.HDUList.writeto](https://docs.astropy.org/en/stable/io/fits/api/hdulists.html#astropy.io.fits.HDUList.writeto)  
+
+#### 新写法
+ ```python
+from csst_fs import fsspec_HDUList
+fsspec_HDUList.writeto(hdul_img, out_combined_img, overwrite=True)
+fsspec_HDUList.writeto(hdul_img, out_combined_img, s3_options=s3_options, overwrite=True)
+```
+
+### table.Table.read
+#### 老写法
+```python
+from astropy import table
+table.Table.read(out_gaia_ldac, hdu=2)
+```
+usage reference:
+[https://docs.astropy.org/en/stable/api/astropy.table.Table.html#astropy.table.Table.read](https://docs.astropy.org/en/stable/api/astropy.table.Table.html#astropy.table.Table.read
+)   
+
+#### 新写法
+```python
+from csst_fs import fsspec_table
+fsspec_table.read(out_gaia_ldac, hdu=2)
+fsspec_table.read(out_gaia_ldac, s3_options=s3_options, hdu=2)
+```
+
+### table.Table.read
+#### 老写法
+ ```python
+ps.write(ref, format='fits', overwrite=True)
+```
+usage reference:
+[https://docs.astropy.org/en/stable/api/astropy.table.Table.html#astropy.table.Table.write](https://docs.astropy.org/en/stable/api/astropy.table.Table.html#astropy.table.Table.write)  
+
+#### 新写法
+```python
+from csst_fs import fsspec_table
+fsspec_table.write(ps, ref, format='fits', overwrite=True)
+fsspec_table.write(ps, ref, format='fits', s3_options=s3_options, overwrite=True)
+```
+

csst_fs/__init__.py

+from .fits import fsspec_fits
+from .fits import fsspec_header
+from .fits import fsspec_HDUList
+from .table import fsspec_table
+from . import s3_fs
\ No newline at end of file

csst_fs/fits/fsspec_HDUList.py

+import fsspec
+from ..fsspec_fileobj import open_fileobj
+from ..s3_config import load_s3_options
+
+def writeto(fits_HDUList, out_path, s3_options=load_s3_options(), *args, **kwargs):
+    fileobj = open_fileobj(out_path, s3_options, mode='wb')
+    fits_HDUList.writeto(fileobj, *args, **kwargs)
+    if hasattr(fileobj, 'close'):
+        fileobj.close()
+    
\ No newline at end of file

csst_fs/fits/fsspec_fits.py

+import fsspec
+from astropy.io import fits
+from ..fsspec_fileobj import open_fileobj
+from ..s3_config import load_s3_options
+
+def open(filename, s3_options=load_s3_options()):
+    return fits.open(filename, fsspec_kwargs=s3_options)
+
+def getdata(filename, s3_options=load_s3_options(), *args, **kwargs):
+    fileobj = open_fileobj(filename, s3_options, mode='rb')
+    return fits.getdata(fileobj, *args, **kwargs)
+
+def getheader(filename, s3_options=load_s3_options(), *args, **kwargs):
+    fileobj = open_fileobj(filename, s3_options, mode='rb')
+    return fits.getheader(fileobj, *args, **kwargs)
\ No newline at end of file

csst_fs/fits/fsspec_header.py

+import fsspec
+from astropy.io import fits
+from ..fsspec_fileobj import open_fileobj
+from ..s3_config import load_s3_options
+
+def tofile(fits_header, out_path, s3_options=load_s3_options(), *args, **kwargs):
+    fileobj = open_fileobj(out_path, s3_options)
+    fits_header.tofile(fileobj, *args, **kwargs)
+    if hasattr(fileobj, 'close'):
+        fileobj.close()
+
+def fromfile(filename, s3_options=load_s3_options(), *args, **kwargs):
+    fileobj = open_fileobj(filename, s3_options, mode='rb')
+    return fits.Header.fromfile(fileobj, *args, **kwargs)
\ No newline at end of file

csst_fs/fsspec_fileobj.py

+import fsspec
+
+def open_fileobj(path: str, s3_options, mode='w'):
+    if(path.startswith("s3")):
+        s3_fs = fsspec.filesystem('s3', **s3_options)
+        fileobj = s3_fs.open(path, mode=mode).__enter__()
+    else:
+        fileobj = path
+    return fileobj
\ No newline at end of file

csst_fs/s3_config.py

+import os
+import json
+
+default_s3_options = {
+    'key': 'minioadmin', 
+    'secret': 'minioadmin', 
+    'endpoint_url': 'http://localhost:9000/'
+}
+
+def load_from_env():
+    s3_options = {
+        'key': os.getenv('S3_KEY'),
+        'secret': os.getenv('S3_SECRET'),
+        'endpoint_url': os.getenv('S3_ENDPOINT_URL')
+    }
+    return s3_options
+
+def load_s3_options():
+    if 'S3_KEY' in os.environ:
+        return load_from_env()
+    return default_s3_options
\ No newline at end of file

csst_fs/s3_fs.py

+import fsspec
+from .s3_config import load_s3_options
+
+def put(lpath, rpath, recursive=False, callback=fsspec.callbacks.DEFAULT_CALLBACK, maxdepth=None, s3_options=load_s3_options(), **kwargs,): 
+    s3_fs = fsspec.filesystem('s3', **s3_options)
+    s3_fs.put(lpath, rpath, recursive, callback, maxdepth, **kwargs)
+
+def get(rpath, lpath, recursive=False, callback=fsspec.callbacks.DEFAULT_CALLBACK, maxdepth=None, s3_options=load_s3_options(), **kwargs,):
+    s3_fs = fsspec.filesystem('s3', **s3_options)
+    s3_fs.get(rpath, lpath, recursive, callback, maxdepth, **kwargs)
\ No newline at end of file

csst_fs/table/fsspec_table.py

+import fsspec
+from astropy import table
+from ..fsspec_fileobj import open_fileobj
+from ..s3_config import load_s3_options
+
+def read(filename, s3_options=load_s3_options(), *args, **kwargs):
+    fileobj = open_fileobj(filename, s3_options, mode='rb')
+    return table.Table.read(fileobj, *args, **kwargs)
+
+def write(table_to_write: table.Table, filename, s3_options=load_s3_options(), *args, **kwargs):
+    fileobj = open_fileobj(filename, s3_options, mode='wb')
+    return table_to_write.write(fileobj, *args, **kwargs)
\ No newline at end of file

setup.py

+from setuptools import setup, find_packages
+
+setup(
+    name='csst_fs',
+    version='0.1.0',
+    packages=find_packages(),
+    install_requires=[
+        'astropy==5.3',
+        'fsspec==2024.5.0',
+        's3fs==2024.5.0'
+    ],
+    python_requires='>=3.9',
+    description='csst pipeline handle file in local file system and remote s3  file system',
+    long_description=open('README.md', encoding='utf-8').read(),
+    long_description_content_type='text/markdown',
+    url='http://gitee.zhejianglab.com/enterprise/csst-fs',
+    author='Pan Qi',
+    author_email='qipan@zhejianglab.com'
+)