exfilms - npm Package Compare versions

Comparing version 1.2.4 to 1.2.5

CHANGELOG.md

@@ -0,1 +1,8 @@
+## [1.2.5](https://github.com/vmalnathnambiar/exfilms/compare/v1.2.4...v1.2.5) (2024-04-16)
+
+
+### Bug Fixes
+
+* **readme:** minor documentation changes ([b4f6db0](https://github.com/vmalnathnambiar/exfilms/commit/b4f6db0058991e4f899fbd094c878ab53e6ec11c))
+
 ## [1.2.4](https://github.com/vmalnathnambiar/exfilms/compare/v1.2.3...v1.2.4) (2024-04-16)
@@ -2,0 +9,0 @@

docs/how-to-exfilms-the-complete-guide.md

@@ -7,3 +7,3 @@ # How to ExfilMS: The Complete Guide
 2. [Execution of ExfilMS and The Use of Flags](#execution-of-exfilms-and-the-use-of-flags)
-3. [Useful Commands](#useful-commands)
+3. [Useful Flags](#useful-flags)
    - [General](#general)
@@ -37,7 +37,7 @@ - [Specifying Input Data](#specifying-input-data)
 
-The `i`, `--inputDirectory` displayed in the error message is known as a command line argument (or "command" or "flag") that is required for the successful execution of ExfilMS. There are both required and non-required flags available for your use. The inclusion of these flags along with the `exfilms` command will configure and establish the behaviour of the tool for running its extraction (and filtering) process.
+The `i`, `--inputDirectory` displayed in the error message is known as a command line flag (or flag) that is required for the successful execution of ExfilMS. There are both required and non-required flags available for your use. The inclusion of these flags along with the `exfilms` command will configure and establish the behaviour of the tool for running its extraction (and filtering) process.
 
 <br>
 
-## Useful Commands
+## Useful Flags
 
@@ -48,3 +48,3 @@ ### General
 
-Displays a list of available commands along with their descriptions. This is useful for understanding the purpose of each flag.
+Displays a list of available flags along with their descriptions. This is useful for understanding the purpose of each flag.
 
@@ -51,0 +51,0 @@ ```md

package.json

 {
   "name": "exfilms",
-  "version": "1.2.4",
+  "version": "1.2.5",
   "description": "A cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with filtering capabilities.",
@@ -5,0 +5,0 @@ "keywords": [

README.md

 ![ExfilMS](./img/logo.png)\
-[![NPM version][npm-image]][npm-url]
-[![license][license-image]][license-url]
-[![CI status][ci-image]][ci-url]
-[![test coverage][codecov-image]][codecov-url]
-[![semantic release][semantic-image]][semantic-url]
-[![npm download][download-image]][download-url]
+[![NPM][npm-image]][npm-url]
+[![License][license-image]][license-url]
+[![CI/CD][cicd-image]][cicd-url]
+[![CodeCov][codecov-image]][codecov-url]
+[![Semantic-Release][semantic-image]][semantic-url]
+[![Downloads][downloads-image]][downloads-url]
 [![DOI-Zenodo][doi-zenodo-image]][doi-zenodo-url]
@@ -123,7 +123,7 @@
 ```md
-# Using command line arguments
+# Using command line flags
 
 $ exfilms -i "/path/to/input/directory/containing/mzML/data/files/" ...
 
-# Interactive
+# Running interactive mode
 
@@ -138,7 +138,7 @@ $ exfilms -x
 ```md
-# Using command line arguments
+# Using command line flags
 
 $ docker run --rm -it -v "/path/to/input/directory/":/inputDirectory -v "/path/to/output/directory/":/outputDirectory -v "/path/to/log/directory/":/logDirectory exfilms -i /inputDirectory -o /outputDirectory -l /logDirectory ....
 
-# Interactive
+# Running interactive mode
 
@@ -173,3 +173,3 @@ $ docker run --rm -it -v "/path/to/input/directory/":/inputDirectory -v "/path/to/output/directory/":/outputDirectory -v "/path/to/log/directory/":/logDirectory exfilms -x
 >
-> 1. Unable to extract MS data from Bruker EVOQ instruments and SCIEX wiff2 scan files (unsupported format by ProteoWizard).
+> 1. Unable to extract MS data from Bruker EVOQ instruments and SCIEX wiff2 scan files (Unsupported file formats by ProteoWizard).
 >
@@ -180,5 +180,5 @@ > 2. Unable to parse mzML data with a file size > 2GB.
 >
-> 4. Slow output write speed due to build architecture difference (i.e, Intel vs AMD vs ARM) when running ExfilMS with Docker.
+> 4. May have slow output write speed due to build architecture difference (i.e, Intel vs AMD vs ARM) when running ExfilMS with Docker.
 >
-> 5. Unable to perform chromatography filtering as of now.
+> 5. Unable to perform chromatogram filtering as of now.
 
@@ -191,9 +191,6 @@ <br>
 
-Nambiar, V., & Nambiar, S. (2024). ExfilMS (Version 1.2.4) [Computer software]. https://doi.org/10.5281/zenodo.10976761
+Nambiar, V., & Nambiar, S. (2024). ExfilMS (Version 1.2.5) [Computer software]. https://doi.org/10.5281/zenodo.10976761
 
 <br>
 
-<!-- ## API Documentation
-Please refer to our API documentation [here](https://vmalnathnambiar.github.io/exfilms/). -->
-
 ## License
@@ -203,2 +200,5 @@
 
+<!-- ## API Documentation
+Please refer to our API documentation [here](https://vmalnathnambiar.github.io/exfilms/). -->
+
 <!-- URLs used in the markdown document-->
@@ -210,4 +210,4 @@
 [license-url]: https://github.com/vmalnathnambiar/exfilms/blob/main/LICENSE
-[ci-image]: https://github.com/vmalnathnambiar/exfilms/actions/workflows/build-publish.yml/badge.svg
-[ci-url]: https://github.com/vmalnathnambiar/exfilms/actions/workflows/build-publish.yml
+[cicd-image]: https://github.com/vmalnathnambiar/exfilms/actions/workflows/build-publish.yml/badge.svg
+[cicd-url]: https://github.com/vmalnathnambiar/exfilms/actions/workflows/build-publish.yml
 [codecov-image]: https://codecov.io/gh/vmalnathnambiar/exfilms/graph/badge.svg?token=V8O80QXJ5S
@@ -217,4 +217,4 @@ [codecov-url]: https://codecov.io/gh/vmalnathnambiar/exfilms
 [semantic-url]: https://github.com/semantic-release/semantic-release
-[download-image]: https://img.shields.io/npm/dm/exfilms.svg
-[download-url]: https://www.npmjs.com/package/exfilms
+[downloads-image]: https://img.shields.io/npm/dm/exfilms.svg
+[downloads-url]: https://www.npmjs.com/package/exfilms
 [doi-zenodo-image]: https://zenodo.org/badge/DOI/10.5281/zenodo.10976761.svg
@@ -221,0 +221,0 @@ [doi-zenodo-url]: https://doi.org/10.5281/zenodo.10976761

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