cht_utils 2.0.0__py3-none-any.whl

cht_utils/remote/__init__.py

@@ -0,0 +1,4 @@
+"""Remote file transfer utilities (S3, SFTP)."""
+
+from cht_utils.remote.s3 import S3Session as S3Session
+from cht_utils.remote.sftp import SSHSession as SSHSession

cht_utils/remote/s3.py

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+"""AWS S3 client wrapper for file and folder operations."""
+
+import os
+import pathlib
+import tarfile
+from multiprocessing.pool import ThreadPool
+from typing import List
+
+import boto3
+from botocore.exceptions import ClientError
+
+
+class S3Session:
+    """AWS S3 session with upload, download, and management operations.
+
+    Parameters
+    ----------
+    access_key : str
+        AWS access key ID.
+    secret_key : str
+        AWS secret access key.
+    region : str
+        AWS region name.
+    """
+
+    def __init__(self, access_key: str, secret_key: str, region: str) -> None:
+        self.ready = True
+        session = boto3.Session(
+            aws_access_key_id=access_key,
+            aws_secret_access_key=secret_key,
+            region_name=region,
+        )
+        self.s3_client = session.client("s3")
+
+    def upload_file(
+        self, bucket_name: str, file: str, s3_folder: str, quiet: bool = True
+    ) -> None:
+        """Upload a local file to S3.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        file : str
+            Local file path.
+        s3_folder : str
+            Remote folder prefix.
+        quiet : bool
+            Suppress progress output.
+        """
+        s3_key = os.path.join(s3_folder, os.path.basename(file)).replace("\\", "/")
+        self.s3_client.upload_file(file, bucket_name, s3_key)
+        if not quiet:
+            print(f"Uploaded {os.path.basename(file)}")
+
+    def download_file(
+        self,
+        bucket_name: str,
+        s3_folder: str,
+        file: str,
+        local_folder: str,
+        quiet: bool = True,
+    ) -> None:
+        """Download a file from S3.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_folder : str
+            Remote folder prefix.
+        file : str
+            File name to download.
+        local_folder : str
+            Local destination directory.
+        quiet : bool
+            Suppress progress output.
+        """
+        s3_key = os.path.join(s3_folder, os.path.basename(file)).replace("\\", "/")
+        local_path = os.path.join(local_folder, os.path.basename(file))
+        self.s3_client.download_file(bucket_name, s3_key, local_path)
+        if not quiet:
+            print(f"Downloaded {os.path.basename(file)}")
+
+    def download_files(
+        self,
+        bucket_name: str,
+        key_list: List[str],
+        file_list: List[str],
+        quiet: bool = True,
+    ) -> None:
+        """Download multiple files in parallel.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        key_list : List[str]
+            List of S3 keys.
+        file_list : List[str]
+            Corresponding local file paths.
+        quiet : bool
+            Suppress progress output.
+        """
+        pool = ThreadPool()
+        pool.starmap(
+            self.download_file_parallel,
+            [(bucket_name, key, file, quiet) for key, file in zip(key_list, file_list)],
+        )
+
+    def download_file_parallel(
+        self, bucket_name: str, s3_key: str, file: str, quiet: bool = True
+    ) -> None:
+        """Download a single file (used for parallel execution).
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_key : str
+            Full S3 key.
+        file : str
+            Local file path.
+        quiet : bool
+            Suppress progress output.
+        """
+        self.s3_client.download_file(bucket_name, s3_key, file)
+        if not quiet:
+            print(f"Downloaded {os.path.basename(file)}")
+
+    def delete_file(
+        self, bucket_name: str, s3_folder: str, file: str, quiet: bool = True
+    ) -> None:
+        """Delete a file from S3.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_folder : str
+            Remote folder prefix.
+        file : str
+            File name to delete.
+        quiet : bool
+            Suppress progress output.
+        """
+        s3_key = os.path.join(s3_folder, os.path.basename(file)).replace("\\", "/")
+        self.s3_client.delete_object(Bucket=bucket_name, Key=s3_key)
+        if not quiet:
+            print(f"Deleted {os.path.basename(file)}")
+
+    def make_folder(self, bucket_name: str, s3_folder: str, quiet: bool = True) -> None:
+        """Create a folder (prefix) in S3.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_folder : str
+            Folder prefix to create.
+        quiet : bool
+            Suppress progress output.
+        """
+        self.s3_client.put_object(Bucket=bucket_name, Key=f"{s3_folder}/")
+        if not quiet:
+            print(f"Made folder: {s3_folder}")
+
+    def upload_folder(
+        self,
+        bucket_name: str,
+        local_folder: str,
+        s3_folder: str,
+        parallel: bool = True,
+        quiet: bool = True,
+    ) -> None:
+        """Recursively upload a local directory to S3.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        local_folder : str
+            Local directory to upload.
+        s3_folder : str
+            Remote folder prefix.
+        parallel : bool
+            Use parallel uploads.
+        quiet : bool
+            Suppress progress output.
+        """
+        local_folder = local_folder.replace("\\", "/")
+        flist = _list_all_files(local_folder)
+        args = [
+            (f, local_folder, s3_folder, bucket_name, self.s3_client, quiet)
+            for f in flist
+        ]
+        if parallel:
+            pool = ThreadPool()
+            pool.starmap(_upload_file, args)
+        else:
+            for a in args:
+                _upload_file(*a)
+
+    def download_folder(
+        self,
+        bucket_name: str,
+        s3_folder: str,
+        local_folder: str,
+        parallel: bool = True,
+        quiet: bool = True,
+    ) -> None:
+        """Download all files under an S3 prefix to a local directory.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_folder : str
+            Remote folder prefix.
+        local_folder : str
+            Local destination directory.
+        parallel : bool
+            Currently unused (sequential download).
+        quiet : bool
+            Suppress progress output.
+        """
+        os.makedirs(local_folder, exist_ok=True)
+        objects = self.s3_client.list_objects(Bucket=bucket_name, Prefix=s3_folder)
+        for obj in objects.get("Contents", []):
+            s3_key = obj["Key"]
+            local_path = os.path.join(local_folder, os.path.basename(s3_key))
+            self.s3_client.download_file(bucket_name, s3_key, local_path)
+            if not quiet:
+                print(f"Downloaded {os.path.basename(s3_key)}")
+
+    def delete_folder(self, bucket_name: str, s3_folder: str) -> None:
+        """Delete all objects under an S3 prefix.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_folder : str
+            Remote folder prefix.
+        """
+        if not s3_folder.endswith("/"):
+            s3_folder += "/"
+        objects = self.s3_client.list_objects(Bucket=bucket_name, Prefix=s3_folder)
+        for obj in objects.get("Contents", []):
+            self.s3_client.delete_object(Bucket=bucket_name, Key=obj["Key"])
+
+    def list_folders(self, bucket_name: str, s3_folder: str) -> List[str]:
+        """List immediate subfolders under an S3 prefix.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_folder : str
+            Remote folder prefix.
+
+        Returns
+        -------
+        List[str]
+            Subfolder names.
+        """
+        if not s3_folder.endswith("/"):
+            s3_folder += "/"
+        folders = []
+        paginator = self.s3_client.get_paginator("list_objects_v2")
+        for page in paginator.paginate(
+            Bucket=bucket_name, Prefix=s3_folder, Delimiter="/"
+        ):
+            for subfolder in page.get("CommonPrefixes", []):
+                folders.append(subfolder["Prefix"].rstrip("/").split("/")[-1])
+        return folders
+
+    def list_files(self, bucket_name: str, s3_folder: str) -> List[str]:
+        """List all file keys under an S3 prefix.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_folder : str
+            Remote folder prefix.
+
+        Returns
+        -------
+        List[str]
+            Full S3 keys.
+        """
+        all_files = []
+        paginator = self.s3_client.get_paginator("list_objects_v2")
+        for page in paginator.paginate(Bucket=bucket_name, Prefix=s3_folder):
+            for obj in page.get("Contents", []):
+                all_files.append(obj["Key"])
+        return all_files
+
+    def download_and_extract_tgz(
+        self, bucket_name: str, s3_folder: str, local_folder: str
+    ) -> None:
+        """Download and extract a ``.tgz`` archive from S3.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_folder : str
+            S3 key of the ``.tgz`` file.
+        local_folder : str
+            Local directory to extract into.
+        """
+        local_tgz_path = os.path.join("/tmp", os.path.basename(s3_folder))
+        self.s3_client.download_file(bucket_name, s3_folder, local_tgz_path)
+        with tarfile.open(local_tgz_path, "r:gz") as tar:
+            tar.extractall(path=local_folder)
+        os.remove(local_tgz_path)
+
+    def check_file_exists(self, bucket_name: str, s3_key: str) -> bool:
+        """Check if a file exists in S3.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_key : str
+            Full S3 key.
+
+        Returns
+        -------
+        bool
+        """
+        try:
+            self.s3_client.head_object(Bucket=bucket_name, Key=s3_key)
+            return True
+        except ClientError as e:
+            if e.response["Error"]["Code"] == "404":
+                return False
+            raise
+
+    def check_folder_exists(self, bucket_name: str, s3_key: str) -> bool:
+        """Check if a folder (prefix) exists in S3.
+
+        Parameters
+        ----------
+        bucket_name : str
+            S3 bucket name.
+        s3_key : str
+            S3 prefix to check.
+
+        Returns
+        -------
+        bool
+        """
+        response = self.s3_client.list_objects_v2(
+            Bucket=bucket_name, Prefix=s3_key, Delimiter="/"
+        )
+        return "CommonPrefixes" in response
+
+
+def _list_all_files(src: str) -> List[str]:
+    """Recursively list all files in a directory."""
+    return [str(f) for f in pathlib.Path(src).rglob("*") if f.is_file()]
+
+
+def _upload_file(
+    file: str,
+    local_folder: str,
+    s3_folder: str,
+    bucket_name: str,
+    s3_client: object,
+    quiet: bool,
+) -> None:
+    """Upload a single file, preserving relative path structure."""
+    relative = file.replace("\\", "/").replace(local_folder, "")
+    s3_key = s3_folder + relative
+    s3_client.upload_file(file, bucket_name, s3_key)
+    if not quiet:
+        print(f"Uploaded {file}")

cht_utils/remote/sftp.py

@@ -0,0 +1,192 @@
+"""SSH/SFTP client for remote file operations."""
+
+import os
+import posixpath
+import socket
+from stat import S_ISDIR
+from typing import Optional
+
+import paramiko
+
+
+class SSHSession:
+    """SSH session with SFTP file transfer capabilities.
+
+    Parameters
+    ----------
+    hostname : str
+        Remote host address.
+    username : str
+        SSH username.
+    key_file : str or None
+        Path to private key file (not yet implemented).
+    password : str or None
+        SSH password.
+    """
+
+    def __init__(
+        self,
+        hostname: str,
+        username: str = "root",
+        key_file: Optional[str] = None,
+        password: Optional[str] = None,
+    ) -> None:
+        self.sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+        self.sock.connect((hostname, 22))
+        self.t = paramiko.Transport(self.sock)
+        self.t.start_client()
+        self.t.auth_password(username, password, fallback=False)
+        self.sftp = paramiko.SFTPClient.from_transport(self.t)
+
+    def command(self, cmd: str) -> str:
+        """Execute a remote command.
+
+        Parameters
+        ----------
+        cmd : str
+            Command string (may contain newlines for multiple commands).
+
+        Returns
+        -------
+        str
+            Combined server response.
+        """
+        chan = self.t.open_session()
+        chan.get_pty()
+        chan.invoke_shell()
+        chan.settimeout(20.0)
+        ret = ""
+        try:
+            ret += chan.recv(1024).decode()
+        except Exception:
+            chan.send("\n")
+            ret += chan.recv(1024).decode()
+        for line in cmd.split("\n"):
+            chan.send(line.strip() + "\n")
+            ret += chan.recv(1024).decode()
+        return ret
+
+    def put(self, localfile: str, remotefile: str) -> None:
+        """Upload a file.
+
+        Parameters
+        ----------
+        localfile : str
+            Local file path.
+        remotefile : str
+            Remote destination path.
+        """
+        self.sftp.put(localfile, remotefile)
+
+    def put_all(self, localpath: str, remotepath: str) -> None:
+        """Recursively upload a directory.
+
+        Parameters
+        ----------
+        localpath : str
+            Local directory to upload.
+        remotepath : str
+            Remote destination directory.
+        """
+        current_path = os.getcwd()
+        os.chdir(os.path.split(localpath)[0])
+        parent = os.path.split(localpath)[1]
+        for walker in os.walk(parent):
+            try:
+                self.sftp.mkdir(remotepath + "/" + walker[0].replace("\\", "/"))
+            except OSError:
+                pass
+            for file in walker[2]:
+                remote_file = f"{remotepath}/{walker[0]}/{file}".replace("\\", "/")
+                self.put(os.path.join(walker[0], file), remote_file)
+        os.chdir(current_path)
+
+    def get(self, remotefile: str, localfile: str) -> None:
+        """Download a file.
+
+        Parameters
+        ----------
+        remotefile : str
+            Remote file path.
+        localfile : str
+            Local destination path.
+        """
+        self.sftp.get(remotefile, localfile)
+
+    def sftp_walk(self, remotepath: str):
+        """Walk a remote directory tree (like ``os.walk``).
+
+        Parameters
+        ----------
+        remotepath : str
+            Remote directory path.
+
+        Yields
+        ------
+        tuple of (str, list, list)
+            ``(path, folders, files)`` for each directory level.
+        """
+        files = []
+        folders = []
+        for f in self.sftp.listdir_attr(remotepath):
+            if S_ISDIR(f.st_mode):
+                folders.append(f.filename)
+            else:
+                files.append(f.filename)
+        yield remotepath, folders, files
+        for folder in folders:
+            new_path = os.path.join(remotepath, folder).replace("\\", "/")
+            yield from self.sftp_walk(new_path)
+
+    def get_all(self, remotepath: str, localpath: str) -> None:
+        """Recursively download a directory.
+
+        Parameters
+        ----------
+        remotepath : str
+            Remote directory path.
+        localpath : str
+            Local destination directory.
+        """
+        self.sftp.chdir(os.path.split(remotepath)[0])
+        parent = os.path.split(remotepath)[1]
+        os.makedirs(localpath, exist_ok=True)
+        for walker in self.sftp_walk(parent):
+            local_dir = os.path.join(localpath, walker[0])
+            os.makedirs(local_dir, exist_ok=True)
+            for file in walker[2]:
+                self.get(
+                    os.path.join(walker[0], file),
+                    os.path.join(localpath, walker[0], file),
+                )
+
+    def write_command(self, text: str, remotefile: str) -> None:
+        """Write text to a remote file and make it executable.
+
+        Parameters
+        ----------
+        text : str
+            Script content.
+        remotefile : str
+            Remote file path.
+        """
+        self.sftp.open(remotefile, "w").write(text)
+        self.sftp.chmod(remotefile, 0o755)
+
+    def rmtree(self, remotepath: str, level: int = 0) -> None:
+        """Recursively delete a remote directory tree.
+
+        Parameters
+        ----------
+        remotepath : str
+            Remote directory to remove.
+        level : int
+            Recursion depth (internal use).
+        """
+        for f in self.sftp.listdir_attr(remotepath):
+            rpath = posixpath.join(remotepath, f.filename)
+            if S_ISDIR(f.st_mode):
+                self.rmtree(rpath, level=level + 1)
+            else:
+                self.sftp.remove(rpath)
+        self.sftp.rmdir(remotepath)

cht_utils-2.0.0.dist-info/METADATA

@@ -0,0 +1,30 @@
+Metadata-Version: 2.4
+Name: cht_utils
+Version: 2.0.0
+Summary: Utility functions for the Coastal Hazards Toolkit
+Author-email: Maarten van Ormondt <maarten.vanormondt@deltares-usa.us>
+License: MIT
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Hydrology
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: boto3
+Requires-Dist: contextily
+Requires-Dist: geopandas
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: pandas
+Requires-Dist: paramiko
+Requires-Dist: pillow
+Requires-Dist: pyproj
+Requires-Dist: pyyaml
+Requires-Dist: scipy
+Requires-Dist: shapely
+Requires-Dist: rioxarray
+Requires-Dist: rasterio
+Requires-Dist: xarray
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Dynamic: license-file

cht_utils-2.0.0.dist-info/RECORD

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+cht_utils/probabilistic/prob_maps.py,sha256=UQacy6duEAmo903V8iRJMtanXQ2RJDD4a7xZZ-AxYzo,7643
+cht_utils/remote/__init__.py,sha256=BYocLmXAnwiVIlMv8arm9nUCqVNiGKeLi3t7EDlaO0w,164
+cht_utils/remote/s3.py,sha256=-bgHiM-fMyjbAz_42lXBo2FWPL0avc0ltky2VGsk80Q,11226
+cht_utils/remote/sftp.py,sha256=TnPSWBM4dN-ZgoXFO0SuFO5x6uCJ8FZSVrkMjBirBrY,5671
+cht_utils-2.0.0.dist-info/licenses/LICENSE,sha256=6KO9er0UAa3Z1wCOaIG9VXUYi9tyKTRtQtWHJ_U4Iwg,1074
+cht_utils-2.0.0.dist-info/METADATA,sha256=G-bZ4NkB1RcnWVKrohVkJr-egY3JE2LRS2hzwgh3aKk,863
+cht_utils-2.0.0.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+cht_utils-2.0.0.dist-info/top_level.txt,sha256=RNQ7P87dotxpkPVIDZ2hDGzcBOPWT1FJKCCctYCNzZ8,10
+cht_utils-2.0.0.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
+cht_utils-2.0.0.dist-info/RECORD,,

cht_utils-2.0.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

cht_utils-2.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 maartenvanormondt
+
+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.

cht_utils-2.0.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+cht_utils

cht_utils-2.0.0.dist-info/zip-safe

@@ -0,0 +1 @@
+