switch to token based publishing

Signed-off-by: Ayush Kamat <[email protected]>

Author: ayushkamat

.gitignore

@@ -19,3 +19,4 @@ docs/build
 scratch.py
 /scratch
 .latch_report.tar.gz
+/credentials

Justfile

@@ -8,7 +8,7 @@ _build:
   python3 setup.py sdist bdist_wheel
 
 _upload:
-  twine upload dist/*
+  twine upload dist/* -u __token__ -p $(<credentials/pypi_token)
 
 build: _clear _build
 

README.md

@@ -15,18 +15,17 @@ scalable computing infrastructure.
 [Slack Community](https://join.slack.com/t/latchbiosdk/shared_invite/zt-193ibmedi-WB6mBu2GJ2WejUHhxMOuwg) • [Docs](https://docs.latch.bio) • [Installation](#installation) •
 [Quickstart](#configuration) • [Latch](https://latch.bio) • [Latch Verified](https://github.com/latch-verified)
 
-
 ![side-by-side](static/side-by-side.png)
 
 </div>
 
 Workflows developed with the SDK feature:
 
-  * Instant no-code interfaces for accessibility and publication
-  * First class static typing
-  * Containerization + versioning of every registered change
-  * Reliable + scalable managed cloud infrastructure
-  * Single line definition of arbitrary resource requirements (eg. CPU, GPU) for serverless execution
+  + Instant no-code interfaces for accessibility and publication
+  + First class static typing
+  + Containerization + versioning of every registered change
+  + Reliable + scalable managed cloud infrastructure
+  + Single line definition of arbitrary resource requirements (eg. CPU, GPU) for serverless execution
 
 The Latch SDK is a framework to build workflows. A collection of existing and
 maintained workflows for common biological assays can be found at [Latch
@@ -38,35 +37,35 @@ Getting your hands dirty with SDK is the best way to understand how it works.
 Run the following three commands in your terminal to register your first
 workflow to LatchBio.
 
-**Prerequisite**: ensure that `docker` is present and running on your machine. 
+**Prerequisite**: ensure that `docker` is present and running on your machine.
 (Install docker [here](https://docs.docker.com/get-docker/) if you don't already
 have it installed.)
 
-First, install latch through `pip`.
+First, install latch through `pip` .
 
-```
+```shell
 $ python3 -m pip install latch
 ```
 
 Then, create some boilerplate code for your new workflow.
 
-```
+```shell
 $ latch init testworkflow
 ```
 
 Finally register the boilerplate code to [LatchBio](latch.bio).
 
-```
+```shell
 $ latch register testworkflow
 ```
 
 This might take 3-10 minutes depending on your network connection. (Subsequent
 registers will complete in seconds by reusing the image layers from this initial
 register.) The registration process will:
 
-  * Build a docker image containing your workflow code
-  * Serialize your code and register it with your LatchBio account
-  * Push your docker image to a managed container registry
+  + Build a docker image containing your workflow code
+  + Serialize your code and register it with your LatchBio account
+  + Push your docker image to a managed container registry
 
 When registration has completed, you should be able to navigate
 [here](https://console.latch.bio/workflows) and see your new workflow in your
@@ -80,7 +79,7 @@ file an issue on [github](https://github.com/latchbio/latch).
 ### Installation
 
 The SDK is distributed on pip. Install in a fresh virtual environment for best
-behavior. 
+behavior.
 
 [Virtualenvwrapper](https://virtualenvwrapper.readthedocs.io/en/latest/) is recommended.
 
@@ -94,29 +93,27 @@ _Note that a local installation of docker is required to register workflows_.
 
 ### Examples
 
-[Latch Verified](https://github.com/latch-verified) features list of well-curated workflows developed by the Latch team. 
+[Latch Verified](https://github.com/latch-verified) features list of well-curated workflows developed by the Latch team.
 * [Bulk RNA-seq](https://github.com/latch-verified/bulk-rnaseq)
 * [Differential Expression](https://github.com/latch-verified/diff-exp)
 * [Pathway Analysis](https://github.com/latch-verified/pathway)
 
 We'll maintain a growing list of well documented examples developed by our community members here. Please open a pull request to feature your own:
 
 **Gene Editing**
-  * [Guide Counter](https://github.com/latchbio/wf-guide_counter)
-  * [Batch-GE: Gene editing analysis](https://github.com/latchbio/wf-batch_ge)
+  + [Guide Counter](https://github.com/latchbio/wf-guide_counter)
+  + [Batch-GE: Gene editing analysis](https://github.com/latchbio/wf-batch_ge)
 
 **Phylogenetics**
-  * [Seq-to-tree: Evolutionary history inference](https://github.com/JLSteenwyk/latch_wf_seq_to_tree)
-  * [Codon optimization estimation](https://github.com/JLSteenwyk/latch_wf_codon_optimization)
-  * [Metamage: Taxonomy classification](https://github.com/jvfe/metamage_latch)
+  + [Seq-to-tree: Evolutionary history inference](https://github.com/JLSteenwyk/latch_wf_seq_to_tree)
+  + [Codon optimization estimation](https://github.com/JLSteenwyk/latch_wf_codon_optimization)
+  + [Metamage: Taxonomy classification](https://github.com/jvfe/metamage_latch)
 
 **Single-cell Analysis**
-  * [ArchR: Single-cell chromatin accessibility analysis](https://github.com/aa20g217/Archr-Latch-Wf)
-  * [emptydropsR: Ambient RNA detection](https://github.com/mrland99/emptydropsR-latch-wf)
-  * [scVelo: Single-cell RNA velocity analysis](https://github.com/aa20g217/RNA-velocity-Latch-WF)
+  + [ArchR: Single-cell chromatin accessibility analysis](https://github.com/aa20g217/Archr-Latch-Wf)
+  + [emptydropsR: Ambient RNA detection](https://github.com/mrland99/emptydropsR-latch-wf)
+  + [scVelo: Single-cell RNA velocity analysis](https://github.com/aa20g217/RNA-velocity-Latch-WF)
 
 **Protein Engineering**
-  * [UniRep: mLSTM "babbler" deep representation learner for protein engineering](https://github.com/matteobolner/unirep_latch)
-  * [FAMSA: Multiple sequence protein alignment](https://github.com/shivaramakrishna99/famsa-latch)
- 
-  
+  + [UniRep: mLSTM "babbler" deep representation learner for protein engineering](https://github.com/matteobolner/unirep_latch)
+  + [FAMSA: Multiple sequence protein alignment](https://github.com/shivaramakrishna99/famsa-latch)