Add CLI (#46)

* add cli

* fix windows path

* add cli

README.md

@@ -55,4 +55,11 @@ db.add(znh5md.io.AtomsReader(atoms))
 
 data = znh5md.ASEH5MD("db.h5")
 data.get_atoms_list() == atoms
-```
+```
+
+## CLI
+ZnH5MD provides a small set of CLI tools:
+
+- `znh5md view <file.h5>` to view the File using `ase.visualize`
+- `znh5md export <file.h5> <file.xyz>` to export the file to `.xyz` or any other supported file format
+- `znh5md convert <file.xyz> <file.h5>` to save a `file.xyz` as `file.h5` in the H5MD standard.

pyproject.toml

@@ -12,6 +12,7 @@ h5py = "^3.7.0"
 dask = {extras = ["array"], version = "^2022.11.1"}
 ase = "^3.22.1"
 tqdm = "^4.65.0"
+typer = "^0.7.0"
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.1.0"
@@ -25,6 +26,8 @@ coverage = "^7.1.0"
 [tool.poetry.group.notebook.dependencies]
 jupyterlab = "^3.5.0"
 
+[tool.poetry.scripts]
+znh5md = 'znh5md.cli:app'
 
 [build-system]
 requires = ["poetry-core"]

znh5md/cli.py

@@ -0,0 +1,60 @@
+import typer
+import importlib.metadata
+import ase.io
+import ase.visualize
+import tqdm
+import pathlib
+
+app = typer.Typer()
+
+
+@app.command()
+def view(file: str):
+    """Use ASE GUI to view a H5MD Trajectory."""
+    import znh5md
+
+    typer.echo(f"Loading atoms from {file}")
+
+    data = znh5md.ASEH5MD(file)
+    ase.visualize.view(data.get_atoms_list())
+
+
+@app.command()
+def export(file: str, output: str):
+    """export a H5MD File into the output file."""
+    import znh5md
+
+    data = znh5md.ASEH5MD(file)
+    for atom in tqdm.tqdm(data.get_atoms_list(), ncols=120):
+        ase.io.write(output, atom, append=True)
+
+
+@app.command()
+def convert(file: str, db_file: str):
+    """Save a trajectory as H5MD File."""
+    import znh5md
+
+    db = znh5md.io.DataWriter(db_file)
+    if not pathlib.Path(db_file).exists():
+        db.initialize_database_groups()
+
+    db.add(znh5md.io.ASEFileReader(file))
+
+
+def version_callback(value: bool) -> None:
+    """Get the installed dask4dvc version."""
+    if value:
+        typer.echo(f"znh5md {importlib.metadata.version('znh5md')}")
+        raise typer.Exit()
+
+
+@app.callback()
+def main(
+    version: bool = typer.Option(
+        None, "--version", callback=version_callback, is_eager=True
+    ),
+) -> None:
+    """Dask4DVC CLI callback.
+    Run the DVC graph or DVC experiments in parallel using dask.
+    """
+    _ = version  # this would be greyed out otherwise

znh5md/format/__init__.py

@@ -31,11 +31,22 @@ class GRP:
 
     @staticmethod
     def encode_boundary(value) -> np.ndarray:
-        return np.array(["periodic".encode() if x else "none".encode() for x in value])
+        return np.array(
+            [
+                (
+                    "periodic".encode(encoding="utf-8")
+                    if x
+                    else "none".encode(encoding="utf-8")
+                )
+                for x in value
+            ]
+        )
 
     @staticmethod
     def decode_boundary(value) -> np.ndarray:
-        pbc = np.array([x == "periodic".encode() for x in value]).astype(bool)
+        pbc = np.array([x == "periodic".encode(encoding="utf-8") for x in value]).astype(
+            bool
+        )
         return pbc
 
 

znh5md/io/base.py

@@ -1,7 +1,6 @@
 import abc
 import dataclasses
 import logging
-import os
 import typing
 
 import h5py
@@ -157,7 +156,7 @@ def yield_chunks(
 @dataclasses.dataclass
 class DataWriter:
     filename: str
-    atoms_path: str = os.path.join("particles", "atoms")
+    atoms_path: str = "particles/atoms"
 
     def initialize_database_groups(self):
         """Create all groups that are required.

znh5md/io/reader.py

@@ -130,7 +130,7 @@ def yield_chunks(
                         # if the property was specifically selected, raise the error
                         raise err
                     else:
-                        log.warning(f"Skipping {name} because {err}")
+                        log.debug(f"Skipping {name} because {err}")
             yield data
             start_index = stop_index
             pbar.update(self.frames_per_chunk)