Update the docs

CITATION.cff

@@ -0,0 +1,39 @@
+# Copyright (C) 2024 Roberto Rossini <roberros@uio.no>
+#
+# SPDX-License-Identifier: MIT
+
+cff-version: 1.2.0
+message: 'If you use this software, please cite it using the metadata from this file.'
+authors:
+  - given-names: Roberto
+    family-names: Rossini
+    orcid: 'https://orcid.org/0000-0003-3096-1470'
+    email: roberros@uio.no
+    affiliation: 'Department of Biosciences, University of Oslo'
+title: hictkpy
+abstract: 'Python bindings for hictk.'
+doi: '10.5281/zenodo.8220299'
+url: 'https://github.com/paulsengroup/hictkpy'
+repository-code: 'https://github.com/paulsengroup/hictkpy'
+type: software
+license: MIT
+preferred-citation:
+  type: article
+  authors:
+  - given-names: Roberto
+    family-names: Rossini
+    orcid: 'https://orcid.org/0000-0003-3096-1470'
+    email: roberros@uio.no
+    affiliation: 'Department of Biosciences, University of Oslo'
+  - given-names: Jonas
+    family-names: Paulsen
+    orcid: 'https://orcid.org/0000-0002-7918-5495'
+    email: jonas.paulsen@ibv.uio.no
+    affiliation: 'Department of Biosciences, University of Oslo'
+  doi: '10.1101/2023.11.26.568707'
+  url: 'https://doi.org/10.1101/2023.11.26.568707'
+  journal: 'Cold Spring Harbor Laboratory'
+  year: 2023
+  month: 11
+  title: 'hictk: blazing fast toolkit to work with .hic and .cool files'
+  abstract: 'We developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.'

README.md

@@ -44,17 +44,23 @@ The complete documentation for hictkpy API is available [here](https://hictkpy.r
 
 If you use hictkpy in you reaserch, please cite the following publication:
 
-Preprint available soon.
+Roberto Rossini, Jonas Paulsen hictk: blazing fast toolkit to work with .hic and .cool files.
+_bioRxiv_ __2023.11.26.568707__. [https://doi.org/10.1101/2023.11.26.568707](https://doi.org/10.1101/2023.11.26.568707)
 
 <details>
 <summary>BibTex</summary>
 
 ```bibtex
-@misc{hictk,
-author = {Roberto Rossini},
-year = {2023},
-note = {https://github.com/paulsengroup/hictk},
-title = {hictk: blazing fast toolkit to work with .hic and .cool files}
+@article {hictk,
+	author = {Roberto Rossini and Jonas Paulsen},
+	title = {hictk: blazing fast toolkit to work with .hic and .cool files},
+	elocation-id = {2023.11.26.568707},
+	year = {2023},
+	doi = {10.1101/2023.11.26.568707},
+	publisher = {Cold Spring Harbor Laboratory},
+	URL = {https://www.biorxiv.org/content/early/2023/11/27/2023.11.26.568707},
+	eprint = {https://www.biorxiv.org/content/early/2023/11/27/2023.11.26.568707.full.pdf},
+	journal = {bioRxiv}
 }
 ```
 

docs/hictkpy.rst → docs/api/cooler.rst

@@ -1,21 +1,9 @@
+..
+   Copyright (C) 2024 Roberto Rossini <roberros@uio.no>
+   SPDX-License-Identifier: MIT
 
-Python API
-==========
-
-.. py:module:: hictkpy
-.. py:currentmodule:: hictkpy
-
-
-.. autofunction:: is_cooler
-
-.. autofunction:: is_hic
-
-.. autoclass:: File
-   :members:
-   :special-members: __init__
-
-.. autoclass:: PixelSelector
-   :members:
+Cooler API
+##########
 
 .. py:module:: hictkpy.cooler
 .. py:currentmodule:: hictkpy.cooler
@@ -27,3 +15,7 @@ Python API
 .. autoclass:: SingleCellFile
    :members:
    :special-members: __init__
+
+.. autoclass:: FileWriter
+   :members:
+   :special-members: __init__

docs/api/generic.rst

@@ -0,0 +1,21 @@
+..
+   Copyright (C) 2024 Roberto Rossini <roberros@uio.no>
+   SPDX-License-Identifier: MIT
+
+Generic API
+===========
+
+.. py:module:: hictkpy
+.. py:currentmodule:: hictkpy
+
+
+.. autofunction:: is_cooler
+
+.. autofunction:: is_hic
+
+.. autoclass:: File
+   :members:
+   :special-members: __init__
+
+.. autoclass:: PixelSelector
+   :members:

docs/api/hic.rst

@@ -0,0 +1,13 @@
+..
+   Copyright (C) 2024 Roberto Rossini <roberros@uio.no>
+   SPDX-License-Identifier: MIT
+
+Hi-C API
+########
+
+.. py:module:: hictkpy.hic
+.. py:currentmodule:: hictkpy.hic
+
+.. autoclass:: FileWriter
+   :members:
+   :special-members: __init__

docs/api/index.rst

@@ -0,0 +1,15 @@
+..
+   Copyright (C) 2024 Roberto Rossini <roberros@uio.no>
+   SPDX-License-Identifier: MIT
+
+Python API Reference
+####################
+
+hictkpy API is structured as follows:
+
+.. toctree::
+   :maxdepth: 1
+
+   generic
+   cooler
+   hic

docs/index.rst

@@ -39,13 +39,17 @@ discourse:
 
 .. code-block:: bibtex
 
-    @misc{hictk,
-       author = {Roberto Rossini},
-       year = {2023},
-       note = {https://github.com/paulsengroup/hictk},
-       title = {hictk: blazing fast toolkit to work with .hic and .cool files}
-    }
-
+  @article {hictk,
+	  author = {Roberto Rossini and Jonas Paulsen},
+	  title = {hictk: blazing fast toolkit to work with .hic and .cool files},
+	  elocation-id = {2023.11.26.568707},
+	  year = {2023},
+	  doi = {10.1101/2023.11.26.568707},
+	  publisher = {Cold Spring Harbor Laboratory},
+	  URL = {https://www.biorxiv.org/content/early/2023/11/27/2023.11.26.568707},
+	  eprint = {https://www.biorxiv.org/content/early/2023/11/27/2023.11.26.568707.full.pdf},
+	  journal = {bioRxiv}
+  }
 
 .. only:: not latex
 
@@ -62,4 +66,4 @@ discourse:
    :caption: API Reference
    :maxdepth: 1
 
-   hictkpy
+   api/index