First pass of updating Mkdocs website.

CHANGELOG.md

@@ -2,162 +2,162 @@
 
 All notable changes to Neptune will be documented in this file.
 
-## 2.0.0 ##
+## 2.0.0
 
 2024-10-21
 
 This release updates Neptune to Python3, removes DRMAA support, fixes a crash when no signatures are produced, and updates the installation process.
 
-### Changed ###
+### Changed
 
 - Python3 has replaced Python2.
 - Improved and updated the installation process.
 
-### Fixed ###
+### Fixed
 
 - Fixed a crash that occurred when candidate signatures were of such low quality (as a consequence of ambiguous sequence characters) that these regions could not be aligned with themselves using BLAST.
 
-### Removed ###
+### Removed
 
 - DRMAA support.
 
-## 1.2.5 ##
+## 1.2.5
 
 2017-05-03
 
 This release provides fixes for ambiguous crashes and improvements to the code quality.
 
-### Changed ###
+### Changed
 
 - We have made an effort to improve the readability of function comments in the source code.
 
-### Fixed ###
+### Fixed
 
 - When running Neptune in parallel (non-DRMAA mode), runtime errors in forked jobs now correctly inform the calling process instead of hanging forever with no meaningful error message. Additionally, the runtime error message is reported to the user. This relates the a known error in Python 2.7 (https://bugs.python.org/issue9400).
 - Inputs containing no A, C, G, or T characters will now cause an appropriate runtime error with an informative message about this problem.
 - Lowercase characters are no longer ingnored when calculating the GC content of inputs.
 
-## 1.2.4 ##
+## 1.2.4
 
 2017-02-27
 
 This release makes several small improvements, including: reducing the standard output clutter, adding timings to stages, and updating the documentation.
 
-### Added ###
+### Added
 
 - Links in the README to the manual.
 - Walkthrough to the manual.
 - Example data to test the software.
 - Timings for stages.
 
-### Changed ###
+### Changed
 
 - Improved clarity in manual.
 - Codeblocks in the manual.
 
-### Removed ###
+### Removed
 
 - Considerable clutter has been removed from standard output.
 
-## 1.2.3 ##
+## 1.2.3
 
 2016-07-11
 
 This release simplifies the installation process.
 
-### Added ###
+### Added
 
 - A script for automatically installing Debian dependencies.
 
-### Changed ###
+### Changed
 
 - The dependencies have changed. Several are now installed as part of Neptune.
 - The Neptune installation no longer requires security privilages.
 - Neptune may be installed multiple times in multiple locations.
 - NumPy and SciPy are now installed using pip.
 
-### 1.2.2 ###
+## 1.2.2
 
 2016-04-06
 
 This release includes some Galaxy improvements and fixes a signature scoring problem.
 
-### Changed ###
+### Changed
 
 - Galaxy XML files have been updated to use different packages of Python.
 
-### Fixed ###
+### Fixed
 
 - A bug confusing inclusion and exclusion has been fixed.
 
-## 1.2.1 ##
+## 1.2.1
 
 2016-03-23
 
 This release of Neptune adds support for Galaxy.
 
-### Added ###
+### Added
 
 - Galaxy-related files: capsules, XML files.
 
-### Changed ###
+### Changed
 
 - Neptune.py and Execution.py are now compatible with Galaxy.
 
-## 1.2.0 ##
+## 1.2.0
 
 2016-03-18
 
 This release of Neptune allows for execution on a single machine without requiring DRMAA. Furthermore, several command line parameters have been modified.
 
-### Added ###
+### Added
 
 - Neptune may be run in parallel on a single machine without DRMAA.
 - "--version" command line option.
 
-### Changed ###
+### Changed
 
 - Several command-line parameters have been changed.
 - The "--parallelization" / "-p" parameter effects all parallelization.
 - The exclusion score is now displayed as a positive number.
 
-## 1.1.1 ##
+## 1.1.1
 
 2016-02-24
 
 This release of Neptune updates the installation instructions to be more informative.
 
-### Changed ###
+### Changed
 
 - Updated README and manual installation instructions.
 - Modified the style of code examples in the manual.
 
-## 1.1.0 ##
+## 1.1.0
 
 2016-01-19
 
 This release of Neptune introduces a simple signature consolidation step, which consolidates signatures produced from multiple files into a single file. Furthermore, the software has been updated to be compatible with the Slurm scheduler.
 
-### Added ###
+### Added
 
 - Neptune now automatically consolidates signatures into a single file.
 - DRMAA job names.
 - Neptune now maintains DRMAA log files.
 - Added the ability to specify the BLAST seed size.
 
-### Changed ###
+### Changed
 
 - The run receipt has been reorganized.
 - Removed some unneeded output files.
 - Removed some unneeded print statements.
 - Removed the --verbose parameter. There was no functionality.
 
-### Fixed ###
+### Fixed
 
 - Neptune is now compatible with the Slurm scheduler.
 - Updated PEP8/Flake8 code compliance (W503).
 
-## 1.0.0 ##
+## 1.0.0
 
 2015-11-18
 

docs/examples.md

@@ -1,6 +1,6 @@
-# Examples #
+# Examples
 
-## Basic Execution ##
+## Basic Execution
 
 The following basic example will report all of the signatures that are sufficiently shared by the (FASTA) sequences in the inclusion directory and sufficiently absent from the (FASTA) sequences in the exclusion directory. Neptune will automatically calculate many of the parameters used in this execution.
 
@@ -17,7 +17,7 @@ The output of immediate interest will be located in the follow file:
 
 This file will contain a consolidated list of signatures, sorted by their Neptune score, which is a combined estimate of sensitivity and specificity. The signatures with higher scores, near the top of the file, are considered the most discriminatory signatures.
 
-## Faster Execution ##
+## Faster Execution
 
 The following example highlights options that allow Neptune to run faster when running in parallel mode (default). It will attempt to run Neptune on 16 parallel processes (`--parallelization`) and parallelize *k*-mer counting and aggregation into 64 tasks (`--organization`) distributed over the 16 parallel processes available.
 
@@ -30,7 +30,7 @@ neptune
     --organization 3
 ```
 
-## Specifying File Locations ##
+## Specifying File Locations
 
 You may wish to specify particular files used in signature discovery. This may be important when specifying references for signature extraction:
 

docs/extra.css

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docs/format.md

@@ -1,4 +1,4 @@
-# Signature Format #
+# Signature Format
 
 The signatures produced by Neptune are output in FASTA format with additional information in the description line. Signatures are output in the following format:
 
@@ -27,35 +27,35 @@ Where:
 | [POS] | Position | The starting position of the signature in the reference. |
 | [SEQUENCE] | Sequence | The sequence content of the signature. |
 
-## ID ##
+## ID
 
 The signature ID is an __arbitrary__, run-unique ID assigned to the signature. The signatures within the same FASTA file will have unique IDs, relative to each other. However, signatures within multiple output files will have overlapping signature IDs. This will be the case when using multiple references or not specifying any reference files. The signatures within the `consolidated.fasta` output will have unique signature IDs.
 
-## Total Score ##
+## Total Score
 
 Signatures are assigned a score corresponding to their highest-scoring BLAST alignments with all inclusion and exclusion targets, which is a sum of the positive inclusion score (sensitivity) and the negative exclusion component (specificity). This score is maximized when all inclusion targets contain a region exactly matching the entire signature and there exists no exclusion targets that match the signature.
 
-## Inclusion Score ##
+## Inclusion Score
 
 The inclusion score is a non-negative number between 0.00 and 1.00 and relates to the signature's sensitivity. This score is determined by the signature's highest-scoring BLAST alignments with all inclusion targets. The inclusion score is maximized (good) when the signature is found exactly and completely in all inclusion targets and minimized (bad) when the signature is not found whatsoever in any inclusion targets.
 
-## Exclusion Score ##
+## Exclusion Score
 
 The exclusion score is a non-positive number between -1.00 and 0.00 and relates to the signature's specificity. This score is determined by the signature's highest-scoring BLAST alignments with all exclusion targets. The exclusion score is maximized (bad) when the signature is found exactly and completely in all exclusion targets and minimized (good) when the signature is not found whatsoever in any exclusion targets.
 
-## Length ##
+## Length
 
 The length describes the length of the signature in bases. Although this can be calculated from the sequence, it is included in the FASTA description to accommodate other tools.
 
-## Reference ##
+## Reference
 
 The reference describes the sequence identifier of the contig the signature was extracted from. This is useful for determining where the signature lies and what sequence surrounds it.
 
-## Position ##
+## Position
 
 The position describes the base position of the signature within the contig reference it was extracted from. This is useful for determining where the signature lies and what sequence surrounds it.
 
-## Sequence ##
+## Sequence
 
 The sequence describes the sequence content of the signature and follows the specifications of FASTA format. However, the sequence will not contain line breaks, regardless of the sequence length.
 

docs/index.md

@@ -1,24 +1,22 @@
-# Neptune #
+# Neptune
 
 A genomic signature is a genomic locus that is sufficiently represented in an inclusion group, and sufficiently absent from a background, or exclusion group. A signature might correlate genomic features with phenotypic traits, such as the presence of a gene with increased organism pathogenicity.
 
 Neptune locates genomic signatures using an exact *k*-mer matching strategy while accommodating *k*-mer mismatches. The software identifies sequences that are sufficiently represented within inclusion targets and sufficiently absent from exclusion targets. The signature discovery process is accomplished using probabilistic models instead of heuristic strategies. Neptune may be leveraged to reveal discriminatory signature sequences to uniquely delineate one group of organisms, such as isolates associated with a disease cluster or event, from unrelated sporadic or environmental microbes.
 
-## Release ##
-
-## Neptune 2.0.0 ##
+## Neptune v2.0.0
 
 2024-10-21
 
 This release updates Neptune to Python3, removes DRMAA support, fixes a crash when no signatures are produced, and updates the installation process.
 
-## Resources ##
+## Resources
 
 * **Source**: [https://github.com/phac-nml/neptune](https://github.com/phac-nml/neptune)
 * **Installation**: [https://phac-nml.github.io/neptune/install/](https://phac-nml.github.io/neptune/install/)
 * **Walkthrough**: [https://phac-nml.github.io/neptune/walkthrough/](https://phac-nml.github.io/neptune/walkthrough/)
 
-## Contact ##
+## Contact
 
 * **Eric Marinier**: [email protected]
 * **Gary van Domselaar**: [email protected]