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Move tests, create makefile action to run tests on examples (#433)

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* Move tests, create makefile action to run tests on examples

* Correct import file for html files

* Build environment for tests

* Fix the CI

* rearrange CI

* fix find cmd and make sure we don't delete the folder implicitly

* more rearranging

* fix folder permissions and custom sed for subfolders

* add toga wheels files

* re-add missing file

* mirror latest changes in alpha ci

* fix find cmd

* try different fix for find

* remove redundant build

Co-authored-by: mariana <marianameireles@protonmail.com>
Co-authored-by: pww217 <pwilson@anaconda.com>
Co-authored-by: Fabio Pliger <fabio.pliger@gmail.com>
This commit is contained in:
Mariana Meireles
2022-05-26 18:31:38 -03:00
committed by GitHub
parent 2c5ef95027
commit a9470ed9c1
111 changed files with 23 additions and 3969 deletions
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examples/simple_bioinformatics_tool.html Normal file
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<!DOCTYPE html>
<html>
<head>
<meta charset='utf-8'>
<meta http-equiv='X-UA-Compatible' content='IE=edge'>
<title>PyScript — Simple Bioinformatics Example</title>
<meta name='viewport' content='width=device-width, initial-scale=1'>
<link rel='stylesheet' type='text/css' media='screen' href='https://cdn.jsdelivr.net/npm/bulma@0.9.3/css/bulma.min.css'>
<link rel="icon" type="image/png" href="https://user-images.githubusercontent.com/49681382/166738771-d0c26557-426c-4688-9641-8db5e6b08348.png" />
<script defer src="https://pyscript.net/alpha/pyscript.js"></script>
</head>
<body>
<!-- Header -->
<section class="hero is-primary is-small">
<div class="hero-body">
<p class="title is-3">PyScript — Simple Bioinformatics Example <span class="tag is-white">v.1</span></p>
<p class="subtitle is-6">
Demonstrates the simple use of <a href="https://pyscript.net/" target="_blank"><code>PyScript</code></a>
in <strong>Bioinformatics/Computational Biology</strong> fields!
</p>
</div>
</section>
<!-- Main Content -->
<div class="container is-white is-fluid" style="margin-top:45px">
<p class="title is-3">🧬 DNA Sequence Tool</p>
<!--- DNA Sequence Input -->
<div class="field">
<label class="label">Input DNA Sequence</label>
<div class="control">
<textarea class="textarea" placeholder="GATTACA" id="dna_seq"></textarea>
</div>
</div>
<!-- Operation Selection -->
<label class="label">Pick the operation to be applied</label>
<div class="field has-addons">
<div class="control is-expanded">
<div class="select is-fullwidth">
<select name="operation" id="operation">
<option value="Reverse">Compute the reverse counterpart</option>
<option value="Complement">Compute the complement counterpart</option>
<option value="ReverseComplement">Compute the reverse complement counterpart</option>
</select>
</div>
</div>
<div class="control">
<button id="run" type="button" class="button is-primary" pys-onClick="run">Run!</button>
<button id="clear" type="button" class="button is-danger" pys-onClick="clear">Clear</button>
</div>
</div>
<hr>
<!--- DNA Sequence Output -->
<label class="label">Output for the <code id="operation_name_output">given operation</code></label>
<div id="output"></div>
</div>
<br><br>
<!-- Footer -->
<footer class="footer">
<div class="content has-text-centered">
<p>
Developed by <a href="mailto:furkanmtorun@gmail.com"><strong>Furkan M. Torun (@furkanmtorun)</strong></a>
<br>
<a href="https://github.com/furkanmtorun">GitHub</a>
| <a href="https://scholar.google.com/citations?user=d5ZyOZ4AAAAJ">Google Scholar</a>
| <a href="https://twitter.com/furkanmtorun">Twitter</a>
| <a href="https://www.linkedin.com/in/furkanmtorun/">LinkedIn</a>
</p>
</div>
</footer>
<py-script>
# Define HTML elements and inputs
dna_alphabet = "ATGC"
output = Element("output")
dna_seq_element = Element("dna_seq")
operation_element = Element("operation")
operation_name_output_element = Element("operation_name_output")
# DNA Sequene Operations
def return_reverse(dna_seq):
return dna_seq[::-1]
def return_complement(dna_seq):
return dna_seq.translate(str.maketrans("ATCG", "TAGC"))
def return_reverse_complement(dna_seq):
return dna_seq.translate(str.maketrans("ATCG", "TAGC"))[::-1]
# Check DNA seq is valid
def check_dna_seq(dna_seq):
return all(letter in dna_alphabet for letter in dna_seq.upper())
# Clear the form and output
def clear(*args, **kwargs):
dna_seq_element.clear()
output.clear()
# Run
def run(*args, **kwargs):
dna_seq = dna_seq_element.value
is_dna_seq_valid = check_dna_seq(dna_seq)
if is_dna_seq_valid:
operation_name = operation_element.value
operation_name_output_element.write(operation_name)
# Compute the desired outputs
if operation_name == "Reverse":
output_dna_seq = return_reverse(dna_seq)
elif operation_name == "Complement":
output_dna_seq = return_complement(dna_seq)
elif operation_name == "ReverseComplement":
output_dna_seq = return_reverse_complement(dna_seq)
# Output the result
output.write(output_dna_seq)
elif (dna_seq.strip() == "") or (dna_seq is None):
output.write("No DNA sequence provided")
else:
output.write("Invalid DNA sequence entered")
</py-script>
</body>
</html>