docs: update RtD guides

.github/workflows/ci.yml

@@ -126,38 +126,3 @@ jobs:
       - name: integration test - paired-ended library
         run: htsinfer --cleanup-regime=KEEP_NONE --verbosity=DEBUG tests/files/adapter_{1,2}.fastq
 
-  publish:
-    name: build and publish app image
-    runs-on: ubuntu-latest
-    if: |
-      github.event_name == 'push' && 
-      github.ref == format('refs/heads/{0}', github.event.repository.default_branch)
-
-    steps:
-
-      - name: check out repository
-        uses: actions/checkout@v3
-
-      - name: generate tag
-        run: |
-          echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV
-
-      - name: build and publish image
-        id: docker
-        uses: philips-software/[email protected]
-        with:
-          dockerfile: .
-          image-name: "htsinfer"
-          tags: "latest ${{ env.TAG }}"
-          push-branches: "${{ github.event.repository.default_branch }}"
-        env:
-          REGISTRY_USERNAME: ${{ secrets.DOCKERHUB_LOGIN }}
-          REGISTRY_TOKEN: "${{ secrets.DOCKERHUB_TOKEN }}"
-          DOCKER_ORGANIZATION: ${{ secrets.DOCKERHUB_ORG }}
-          GITHUB_ORGANIZATION: ${{ github.repository_owner }}
-
-      - name: Verify that image was pushed
-        run: |
-          echo "Push indicator: ${{ steps.docker.outputs.push-indicator }}"
-          echo "# Set to 'true' if image was pushed, empty string otherwise"
-          test "${{ steps.docker.outputs.push-indicator }}" == "true"

README.md

@@ -3,26 +3,25 @@
 [![license][badge-license]][badge-url-license]
 [![docs][badge-docs]][badge-url-docs]
 [![release_gh][badge-release-gh]][badge-url-release-gh]
-[![release_docker][badge-release-docker]][badge-url-release-docker]
 [![ci][badge-ci]][badge-url-ci]
 [![coverage][badge-coverage]][badge-url-coverage]
+[![release_biocontainer][badge-release-biocontainer]][badge-url-release-biocontainer]
 [![DOI:zenodo][badge-doi-zenodo]][badge-url-doi-zenodo]
 
-HTSinfer infers metadata from Illumina high-throughput sequencing (HTS) data.
+HTSinfer infers RNA-Seq metadata from Illumina high-throughput sequencing (HTS) data.
 
 ## Quick start
 
 For a more in-depth guide please refer to the [HTSinfer documentation][docs-documentation].
 
 ### Installation
 
-In order to use the HTSinfer, clone the repository and install the
-dependencies via [Conda][conda] or [Mamba][mamba]:
+HTSinfer is available as part of the [Bioconda][bioconda-release] channel, therefore the preferred installation method is via [Mamba][mamba] or [Conda][conda].
+
+To create a new Conda environment with HTSinfer and its dependencies installed, run:
 
 ```sh
-git clone https://github.com/zavolanlab/htsinfer
-cd htsinfer
-conda env create --file environment.yml
+mamba create --name htsinfer bioconda::htsinfer
 ```
 
 Then, activate the `htsinfer` Conda environment with:
@@ -31,27 +30,16 @@ Then, activate the `htsinfer` Conda environment with:
 conda activate htsinfer
 ```
 
+To install HTSinfer in your current environment, run:
+
+```sh
+mamba install bioconda::htsinfer
+```
+
 ### General usage
 
 ```sh
-htsinfer [--output-directory PATH]
-         [--temporary-directory PATH]
-         [--cleanup-regime {DEFAULT,KEEP_ALL,KEEP_NONE,KEEP_RESULTS}]
-         [--records INT]
-         [--threads INT]
-         [--transcripts FASTA]
-         [--read-layout-adapters PATH]
-         [--read-layout-min-match-percentage FLOAT]
-         [--read-layout-min-frequency-ratio FLOAT]
-         [--library-source-min-match-percentage FLOAT]
-         [--library-source-min-frequency-ratio FLOAT]
-         [--library-type-max-distance INT]
-         [--library-type-mates-cutoff FLOAT]
-         [--read-orientation-min-mapped-reads INT]
-         [--read-orientation-min-fraction FLOAT]
-         [--tax-id INT]
-         [--verbosity {DEBUG,INFO,WARN,ERROR,CRITICAL}]
-         [-h] [--version]
+htsinfer [-h] [--verbosity {DEBUG,INFO,WARN,ERROR,CRITICAL}] [--version]       
          PATH [PATH]
 ```
 
@@ -131,22 +119,21 @@ example library:
 }
 ```
 
-To better understand the output, please refer to the [`Results`
-model][docs-api-results] in the [API documentation][badge-url-docs].
+To better understand the output, please refer to the [`Results`][docs-api-results] model in the [API documentation][badge-url-docs].
 
-### API documentation
+## Versioning
 
-Auto-built API documentation is hosted on [ReadTheDocs][badge-url-docs].
+The project follows the [Semantic Versioning][semver] guidelines for version management. Currently, the service is in its beta phase, meaning API breaking changes or updates may occur without prior notice.
 
-### Contributing
+## Contributing
 
 This project lives off your contributions, be it in the form of bug reports,
 feature requests, discussions, or fixes and other code changes. Please refer
 to the [contributing guidelines](CONTRIBUTING.md) if you are interested to
 contribute. Please mind the [code of conduct](CODE_OF_CONDUCT.md) for all
 interactions with the community.
 
-### Contact
+## Contact
 
 For questions or suggestions regarding the code, please use the
 [issue tracker][issue-tracker]. For any other inquiries, please contact us
@@ -158,17 +145,19 @@ by email: <[email protected]>
 [badge-coverage]: <https://codecov.io/gh/zavolanlab/htsinfer/branch/dev/graph/badge.svg?token=KYGJ9MUPHT>
 [badge-docs]: <https://readthedocs.org/projects/htsinfer/badge/?version=latest>
 [badge-license]: <https://img.shields.io/badge/license-Apache%202.0-blue.svg>
-[badge-release-docker]: <https://img.shields.io/docker/image-size/zavolab/htsinfer?color=C39BD3&label=docker>
+[badge-release-biocontainer]: <https://img.shields.io/badge/BioContainer-%20htsinfer-blue?style=flat.svg>
 [badge-release-gh]: <https://img.shields.io/github/v/tag/zavolanlab/htsinfer?color=C39BD3>
 [badge-doi-zenodo]: <https://zenodo.org/badge/265279928.svg>
 [badge-url-ci]: <https://github.com/zavolanlab/htsinfer/actions?query=workflow%3Aci>
 [badge-url-coverage]: <https://codecov.io/gh/zavolanlab/htsinfer>
 [badge-url-docs]: <https://htsinfer.readthedocs.io/en/latest/?badge=latest>
 [badge-url-license]: <http://www.apache.org/licenses/LICENSE-2.0>
-[badge-url-release-docker]: <https://hub.docker.com/repository/docker/zavolab/htsinfer>
+[badge-url-release-biocontainer]: <https://quay.io/repository/biocontainers/htsinfer>
 [badge-url-release-gh]: <https://github.com/zavolanlab/htsinfer/releases>
 [badge-url-doi-zenodo]: <https://doi.org/10.5281/zenodo.13985958>
 [conda]: <https://docs.conda.io/en/latest/miniconda.html>
+[bioconda-release]: <https://anaconda.org/bioconda/htsinfer>
+[semver]: <https://semver.org/>
 [contact]: <https://zavolan.biozentrum.unibas.ch/>
 [docs-documentation]: <https://htsinfer.readthedocs.io/>
 [docs-api-results]: <https://htsinfer.readthedocs.io/en/latest/modules/htsinfer.html#htsinfer.models.Results>

docs/conf.py

@@ -1,4 +1,4 @@
-from htsinfer import __version__
+from htsinfer.version import __version__
 
 # Configuration file for the Sphinx documentation builder.
 #
@@ -48,9 +48,7 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = [
     '_build',
-    'api/yourpackage.rst',
     'setup.py',
-    'Thumbs.db',
     '.DS_Store',
     '.eggs'
 ]

docs/guides/examples.rst

@@ -4,7 +4,7 @@ Examples
 `HTSinfer` provides easy-to-use commands for analyzing single- and paired-ended RNA-Seq libraries.
 
 
-Single-ended Library Example
+Single-ended library example
 ----------------------------
 
 To run `HTSinfer` on a single-ended RNA-Seq library, use the following command:
@@ -13,7 +13,7 @@ To run `HTSinfer` on a single-ended RNA-Seq library, use the following command:
 
    htsinfer tests/files/adapter_single.fastq
 
-Paired-ended Library Example
+Paired-ended library example
 ----------------------------
 
 To run `HTSinfer` on a paired-ended RNA-Seq library, use the following command:
@@ -24,7 +24,7 @@ To run `HTSinfer` on a paired-ended RNA-Seq library, use the following command:
 
 Both commands will output the results in JSON format to :code:`STDOUT` and the log to :code:`STDERR`.
 
-Example Output
+Example output
 --------------
 
 Here is a sample output for the paired-ended library:
@@ -84,4 +84,13 @@ Here is a sample output for the paired-ended library:
       }
    }
 
+Results
+-------
+
 For more details on the output structure, refer to the :code:`Results` model in the API documentation.
+
+- :code:`library_stats`: Read length statistics results, including the minimum, maximum, mean, median and mode.
+- :code:`library_source`: Library source inference results, with the short name and NCBI taxonomy ID of the source organism.
+- :code:`library_type`: Library type inference results, single- or paired-end. In case of paired-end samples, the mate designation.
+- :code:`read_orientation`: Read orientation inference results, based on the fragment library types notation from `Salmon <https://salmon.readthedocs.io/en/latest/library_type.html>`_.
+- :code:`read_layout`: Read layout inference results, including the 3'-adapter sequence and the poly(A) fraction. 

docs/guides/installation.rst

@@ -1,36 +1,56 @@
 Installation
 ============
 
-This section describes how to install `HTSinfer` using Conda.
+This section describes how to install `HTSinfer`.
 
-Clone the Repository and Install Dependencies
----------------------------------------------
+Install using Conda
+-------------------
 
-To install `HTSinfer`, first clone the repository and install the dependencies via `Conda <https://docs.conda.io/en/latest/miniconda.html>`_:
+The easiest and quickest installation method is via `Mamba <https://mamba.readthedocs.io/en/latest/installation.html>`_ or `Conda <https://docs.conda.io/en/latest/miniconda.html>`_.
+`HTSinfer` is available as part of the `Bioconda <https://anaconda.org/bioconda/htsinfer>`_ channel.
+
+To create a new Conda environment with `HTSinfer` and its dependencies installed, run:
+
+.. code-block:: bash
+
+   mamba create --name htsinfer bioconda::htsinfer
+
+
+Then, activate the `htsinfer` Conda environment with:
+
+.. code-block:: bash
+
+   conda activate htsinfer
+
+
+To install `HTSinfer` in your current environment, run:
+
+.. code-block:: bash
+
+   mamba install bioconda::htsinfer
+
+Install from GitHub
+-------------------
+
+If you would like to contribute to the development of `HTSinfer`, or wishing to use unreleased versions, you can install `HTSinfer` from the `GitHub <https://github.com/zavolanlab/htsinfer>`_.
+First clone the repository and install the dependencies via `Conda <https://docs.conda.io/en/latest/miniconda.html>`_:
 
 .. code-block:: bash
 
    git clone https://github.com/zavolanlab/htsinfer.git
    cd htsinfer
-   conda env create --file environment.yml
+   mamba env create --file environment.yml
    # Alternatively, to install with development dependencies,
    # run the following instead
-   conda env create --file environment-dev.ymls
-
-.. note::
-
-   Creating the environment may take some time. It is strongly recommended to install `Mamba <https://mamba.readthedocs.io/en/latest/installation.html>`_ and replace :code:`conda` with :code:`mamba` in the previous commands for faster installation.
-
-Activate the Conda Environment
-------------------------------
+   mamba env create --file environment-dev.ymls
 
 After the installation is complete, activate the :code:`htsinfer` Conda environment with:
 
 .. code-block:: bash
 
    conda activate htsinfer
 
-Verify the Installation (Optional)
+Verify the installation (optional)
 ----------------------------------
 
 If you have installed the development or testing dependencies, you can verify that `HTSinfer` was installed correctly by executing the tests shipped with the package: