Add Chemfiles reader (#38)

* add chemfiles and ase reader

* add chemfiles test

* update test

* pre-commit setup

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update tests

* update READEM.md

* bump version

* support energies

* add cell

* support box

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+default_language_version:
+  python: python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-json
+      - id: check-merge-conflict
+        args: ['--assume-in-merge']
+      - id: check-toml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: ['--fix=lf']
+      - id: sort-simple-yaml
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        additional_dependencies: ["tomli"]
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: 'v0.0.267'
+    hooks:
+      - id: ruff
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.16
+    hooks:
+    - id: mdformat
+      args: ["--wrap=80"]

LICENSE

@@ -248,4 +248,4 @@ CONTRIBUTION AGREEMENT
 
 By contributing to the BVLC/caffe repository through pull-request, comment,
 or otherwise, the contributor releases their content to the
-license and copyright terms herein.
+license and copyright terms herein.

README.md

@@ -5,14 +5,18 @@
 
 # ZnH5MD - High Performance Interface for H5MD Trajectories
 
-ZnH5MD allows easy access to simulation results from H5MD trajectories.
-It provides a Python interface and can convert existing data to H5MD files as well as export to other formats.
+ZnH5MD allows easy access to simulation results from H5MD trajectories. It
+provides a Python interface and can convert existing data to H5MD files as well
+as export to other formats.
+
 ```
 pip install znh5md["dask"]
 ```
 
 ## Example
-In the following example we investigate an H5MD dump from LAMMPS with 1000 atoms and 201 configurations:
+
+In the following example we investigate an H5MD dump from LAMMPS with 1000 atoms
+and 201 configurations:
 
 ```python
 import znh5md
@@ -38,13 +42,19 @@ for item in traj.position.batch(size=27, axis=0):
 ```
 
 ## ASE Atoms
+
 You can use ZnH5MD to store ASE Atoms objects in the H5MD format.
 
-> ZnH5MD does not support all features of ASE Atoms objects. It s important to note that unsupported parts are silently ignored and no error is raised.
+> ZnH5MD does not support all features of ASE Atoms objects. It s important to
+> note that unsupported parts are silently ignored and no error is raised.
 
 > The ASEH5MD interface will not provide any time and step information.
 
-> If you have a list of Atoms with different PBC values, you can use `znh5md.io.AtomsReader(atoms, use_pbc_group=True)`. This will create a `pbc` group in `box/` that also contains `step` and `time`. This is not an official H5MD specification so it can cause issues with other tools. If you don't specify this, the pbc of the first atoms in the list will be applied.
+> If you have a list of Atoms with different PBC values, you can use
+> `znh5md.io.AtomsReader(atoms, use_pbc_group=True)`. This will create a `pbc`
+> group in `box/` that also contains `step` and `time`. This is not an official
+> H5MD specification so it can cause issues with other tools. If you don't
+> specify this, the pbc of the first atoms in the list will be applied.
 
 ```python
 import znh5md
@@ -55,18 +65,24 @@ atoms: list[ase.Atoms]
 db = znh5md.io.DataWriter(filename="db.h5")
 db.initialize_database_groups()
 
-db.add(znh5md.io.AtomsReader(atoms))
+db.add(znh5md.io.AtomsReader(atoms)) # or znh5md.io.ChemfilesReader
 
 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.
+- `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.
 
 ## More examples
-A complete documentation is still work in progress. In the meantime, I can recommend looking at the tests, especially `test_znh5md.py` to learn more about slicing and batching.
+
+A complete documentation is still work in progress. In the meantime, I can
+recommend looking at the tests, especially `test_znh5md.py` to learn more about
+slicing and batching.