scout-browser 4.92__py3-none-any.whl → 4.95.0__py3-none-any.whl

scout/server/blueprints/variants/templates/variants/components.html

@@ -161,94 +161,84 @@
 
 {% macro gene_cell(variant, inherit_palette) %}
   <div class="align-items-center">
-    {% if variant.category == "cancer" or variant.category == "sv_cancer" %}
-      <a data-bs-toggle="tooltip" data-bs-html="true" title="
+
+    {% macro gene_tooltip(gene) %}
+      <div>
         <div>
+          <strong>{{ gene.hgnc_symbol }}</strong>: {{ gene.description }}
+        </div>
+        {% if gene.inheritance %}
           <div>
-            <strong>{{ variant.first_rep_gene.hgnc_symbol }}</strong>: {{ variant.first_rep_gene.description }}
+            <strong>Models</strong>: {{ gene.inheritance|join(',') }}
           </div>
-          {% if variant.first_rep_gene.inheritance %}
-            <div>
-              <strong>Models</strong>: {{ variant.first_rep_gene.inheritance|join(',') }}
-            </div>
-          {% endif %}
-        {% if variant.first_rep_gene.phenotypes %}
+        {% endif %}
+        {% if gene.phenotypes %}
           <div><strong>OMIM disease</strong>
-          {% for disease in variant.first_rep_gene.phenotypes %}
-            <div>
-                {{ disease.description }}
-            </div>
+          {% for disease in gene.phenotypes %}
+            <div>{{ disease.description }}</div>
           {% endfor %}
           </div>
         {% endif %}
-        </div>"
-        {% if variant.first_rep_gene %}
-          href="{{ url_for('genes.gene', hgnc_id=variant.first_rep_gene.hgnc_id) }}"
-        {% endif %}>
-        {{ variant.first_rep_gene.hgnc_symbol or variant.first_rep_gene.hgnc_id }}
-        {% if variant.secondary_gene %}
-          <span class="text-muted">
-            ({{ variant.second_rep_gene.hgnc_symbol or variant.second_rep_gene.hgnc_id }})
-          </span>
-        {% endif %}
+      </div>
+    {% endmacro %}
+
+    {% macro gene_link(gene) %}
+      <a
+        data-bs-toggle="tooltip"
+        data-bs-html="true"
+        title="{{ gene_tooltip(gene) }}"
+        href="{{ url_for('genes.gene', hgnc_id=gene.hgnc_id) }}"
+      >
+        {{ gene.hgnc_symbol or gene.hgnc_id }}
       </a>
+    {% endmacro %}
+
+    {% macro panel_badge(variant, gene_id=0) %}
+
+      {% set matching_panels = [] %}
+      {% for panel in variant.case_panels|rejectattr('removed')|list %}
+        {% if gene_id in panel.hgnc_ids %}
+           {% set _ = matching_panels.append(panel) %}
+        {% endif %}
+      {% endfor %}
 
-      {% set panel_count = variant.case_panels|rejectattr('removed')|list|length %}
-      {% if panel_count > 0%}
-          <a
-            class="badge bg-secondary text-white"
-            data-bs-toggle="popover"
-            data-bs-html="true"
-            data-bs-trigger="hover click"
-            title="Overlapping gene panels"
-            data-bs-content="{% for panel in variant.case_panels|sort(attribute='panel_name',case_sensitive=False)|rejectattr('removed') %}
-              {{ panel.panel_name|safe }}<br>
-              {% endfor %}"
-            >{{panel_count}}
-          </a>
+      {% set panel_count = matching_panels|length %}
+      <a
+        class="badge bg-secondary text-white"
+        data-bs-toggle="popover"
+        data-bs-html="true"
+        data-bs-trigger="hover click"
+        title="Overlapping gene panels"
+        data-bs-content="{% for panel in matching_panels %}
+          {{ panel.panel_name|safe }}<br>
+        {% else %} No ovelapping gene panels {% endfor %}"
+      >{{ panel_count }}</a>
+    {% endmacro %}
+
+    {% if variant.category in ["cancer", "sv_cancer"] %}
+      {% if variant.first_rep_gene %}
+        {{ gene_link(variant.first_rep_gene) }}
+      {% endif %}
+      {% if variant.secondary_gene %}
+        <span class="text-muted">
+          ({{ variant.second_rep_gene.hgnc_symbol or variant.second_rep_gene.hgnc_id }})
+        </span>
+      {% endif %}
+      {% if variant.first_rep_gene or variant.second_rep_gene %}
+        {{ panel_badge(variant, variant.first_rep_gene.hgnc_id or variant.second_rep_gene.hgnc_id) }}
       {% endif %}
     {% else %}
-      {% set panel_count = variant.case_panels|rejectattr('removed')|list|count %}
       {% for gene in variant.genes %}
         <div>
-        <a data-bs-toggle="tooltip" data-bs-html="true" title="
-        <div>
-          <div>
-            <strong>{{ gene.hgnc_symbol }}</strong>: {{ gene.description }}
-          </div>
-          {% if gene.inheritance %}
-            <div>
-              <strong>Models</strong>: {{ gene.inheritance|join(',') }}
-            </div>
-          {% endif %}
-          {% if gene.phenotypes %}
-            <div><strong>OMIM disease</strong>
-            {% for disease in gene.phenotypes %}
-              <div>
-                  {{ disease.description }}
-              </div>
-            {% endfor %}
-            </div>
-          {% endif %}
-        </div>"
-          href="{{ url_for('genes.gene', hgnc_id=gene.hgnc_id) }}">{{ gene.hgnc_symbol or gene.hgnc_id }}
-        {% for model in gene.inheritance %} {{ inheritance_badge(model,inherit_palette) }}{% endfor %}</a>
-        {% if panel_count > 0 %}
-          <a
-            class="badge bg-secondary text-white"
-            data-bs-toggle="popover"
-            data-bs-html="true"
-            data-bs-trigger="hover click"
-            data-bs-content="{% for panel in variant.case_panels|sort(attribute='panel_name',case_sensitive=False)|rejectattr('removed') %}
-              {{ panel.panel_name|safe }}<br>
-              {% endfor %}"
-            title="Overlapping gene panels">{{panel_count}}
-          </a>
-        {% endif %}
-      </div>
+          {{ gene_link(gene) }}
+          {% for model in gene.inheritance %}
+            {{ inheritance_badge(model, inherit_palette) }}
+          {% endfor %}
+          {{ panel_badge(variant, gene.hgnc_id) }}
+        </div>
       {% endfor %}
-
     {% endif %}
+
   </div>
 {% endmacro %}
 
@@ -413,3 +403,17 @@
   <script src="https://cdn.datatables.net/1.12.0/js/jquery.dataTables.min.js" integrity="sha512-fu0WiDG5xqtX2iWk7cp17Q9so54SC+5lk/z/glzwlKFdEOwGG6piUseP2Sik9hlvlmyOJ0lKXRSuv1ltdVk9Jg==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
   <script src="https://cdn.datatables.net/1.12.0/js/dataTables.bootstrap5.min.js" integrity="sha512-nfoMMJ2SPcUdaoGdaRVA1XZpBVyDGhKQ/DCedW2k93MTRphPVXgaDoYV1M/AJQLCiw/cl2Nbf9pbISGqIEQRmQ==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
 {% endmacro %}
+
+{% macro allele_cell(allele) %}
+  {% if 'alt_freq' in allele %}
+    {% if allele.alt_freq == -1 %}
+      <span class="text-body">.</span>
+    {% else %}
+      <span class="text-body"><b>{{ allele.alt_freq|round(4) }}</b></span>
+    {% endif %}
+    <br>
+    <small class="text-body">{% if 'alt_depth' in allele and allele.alt_depth >= 0 %}{{ allele.alt_depth }}{% else %}.{% endif %}|{% if 'ref_depth' in allele and allele.ref_depth >= 0 %}{{ allele.ref_depth }}{% else %}.{% endif %}</small>
+  {% else %}
+    <span class="text-body">N/A</span>
+  {% endif %}
+{% endmacro %}

scout/server/blueprints/variants/templates/variants/indicators.html

@@ -74,6 +74,17 @@
   {% endif %}
 {% endmacro %}
 
+{% macro ccv_evaluations_badge(variant) %}
+  {% if variant.ccv_evaluations %}
+    {% for evaluation in (variant.ccv_evaluations or []) %}
+      <span class="badge bg-secondary" style="margin-left:1px" data-bs-toggle="tooltip" data-bs-placement="right"
+        title="Previously classified as {{ evaluation.ccv_classification.label }}">
+        {{ evaluation.ccv_classification.short }}
+      </span>
+    {% endfor %}
+  {% endif %}
+{% endmacro %}
+
 {% macro dismissals_badge(variant) %}
   {% if variant.dismissals %}
       <span class="badge bg-secondary" style="margin-left:1px" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top"

scout/server/blueprints/variants/templates/variants/sv-variants.html

@@ -108,8 +108,8 @@ onsubmit="return validateForm()">
     </td>
     <td>{{ variant.sub_category|upper }}</td>
     <td>{{ variant.chromosome if variant.chromosome == variant.end_chrom else variant.chromosome+'-'+variant.end_chrom }}</td>
-    <td><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
-<td><span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
+    <td>{% if variant.chromosome != variant.end_chrom %}<span class="text-body"></span><b>{{ variant.chromosome }}</b>:</span>{% endif %}<span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
+    <td>{% if variant.chromosome != variant.end_chrom %}<span class="text-body"><b>{{ variant.end_chrom }}</b>:</span>{% endif %}<span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
     <td class="text-end"><span style="white-space: nowrap;">{{ '-' if variant.length == 100000000000 else variant.length|human_longint|safe}}</span></td>
     <td>
       {{ frequency_cell_general(variant) }}

scout/server/links.py

@@ -714,7 +714,7 @@ def ucsc_link(variant_obj, build=None):
     )
     if build == 38:
         url_template = (
-            "http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg20&"
+            "http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&"
             "position=chr{this[chromosome]}:{this[position]}"
             "-{this[position]}&dgv=pack&knownGene=pack&omimGene=pack"
         )

scout/server/static/custom_images.js

@@ -1,3 +1,11 @@
+const imgMaxWidth = window.innerWidth*0.7;
+const imgMaxHeight = window.innerHeight*0.7;
+
+function calculateAspectRatioFit(srcWidth, srcHeight, maxWidth, maxHeight) {
+    let ratio = Math.min(maxWidth / srcWidth, maxHeight / srcHeight);
+    return [srcWidth*ratio, srcHeight*ratio];
+}
+
 /**
  * This function fetches an image from disk and displays it in a specified div
  * @param {string} imageUrl - The URL of the image to fetch
@@ -9,15 +17,24 @@
 		 .then(blob => {
 				 const img = document.createElement("img");
 				 img.src = URL.createObjectURL(blob);
+				 if (width > imgMaxWidth || height > imgMaxHeight) {
+				 		const resized_pixels = calculateAspectRatioFit(width, height, imgMaxWidth, imgMaxHeight);
+				 		width = resized_pixels[0];
+				 		height = resized_pixels[1];
+				 }
 				 if (width) {
 				 	img.style.width = width+'px';
 				 }
 				 if (height) {
 				 	img.style.height = height+'px';
 				 }
-				 // Display the image in the specified div
+				 // Add the image to a link and add the link to the div
+				 const link = document.createElement('a');
+				 link.appendChild(img);
+				 link.href = img.src;
+				 link.setAttribute('target', "_blank");
 				 const div = document.getElementById(divId);
-				 div.appendChild(img);
+				 div.appendChild(link);
 		})
 		.catch(error => console.error(error));
 }

scout/utils/acmg.py

@@ -1,6 +1,5 @@
 # coding=UTF-8
 
-
 from typing import Optional
 
 from scout.constants import ACMG_COMPLETE_MAP

scout/utils/ccv.py

@@ -0,0 +1,193 @@
+# coding=UTF-8
+from typing import Optional
+
+from scout.constants.ccv import CCV_COMPLETE_MAP, CCV_POTENTIAL_CONFLICTS
+
+
+def get_ccv_points(ccv_terms: set) -> int:
+    """
+    Use the algorithm described in Clingen-CGC-VIGG classification paper (Horak 2022)
+    Given a set of CCV evidence criteria terms
+    for each term,
+      check prefixes if no suffix match or stand-alone criteria match
+
+    O positive, SB negative.
+    VS 8 points, S 4, M 2, P 1.
+
+    If no terms return None
+
+    Args:
+        ccv_terms(set(str)): A collection of prediction terms
+    Returns:
+        points(int):"""
+
+    ovs_terms = []
+    os_terms = []
+    om_terms = []
+    op_terms = []
+    sbvs_terms = []
+    sbs_terms = []
+    sbm_terms = []
+    sbp_terms = []
+
+    prefix_map = {
+        "OVS": ovs_terms,
+        "OS": os_terms,
+        "OM": om_terms,
+        "OP": op_terms,
+        "SBVS": sbvs_terms,
+        "SBS": sbs_terms,
+        "SBM": sbm_terms,
+        "SBP": sbp_terms,
+    }
+
+    suffix_map = {
+        "_Strong": {"O": os_terms, "SB": sbs_terms},
+        "_Moderate": {"O": om_terms, "SB": sbm_terms},
+        "_Supporting": {"O": op_terms, "SB": sbp_terms},
+    }
+
+    for term in ccv_terms:
+        for suffix, prefix_dict in suffix_map.items():
+            if term.endswith(suffix):
+                for prefix, term_list in prefix_dict.items():
+                    if term.startswith(prefix):
+                        term_list.append(term)
+                        break
+                else:
+                    continue
+                break
+        else:
+            for prefix, term_list in prefix_map.items():
+                if term.startswith(prefix):
+                    term_list.append(term)
+                    break
+    points = (
+        8 * len(ovs_terms)
+        + 4 * len(os_terms)
+        + 2 * len(om_terms)
+        + len(op_terms)
+        - 8 * len(sbvs_terms)
+        - 4 * len(sbs_terms)
+        - 2 * len(sbm_terms)
+        - len(sbp_terms)
+    )
+    return points
+
+
+def get_ccv(ccv_terms: set) -> Optional[str]:
+    """Use the algorithm described in Clingen-CGC-VIGG classification paper (Horak 2022)
+
+    If no terms return None
+
+    O >= 10
+    OP 6 <= p <= 9
+    VUS 0 <= p <= 5
+    LB -1 <= p <= -6
+    B <= -7
+
+    Args:
+        ccv_terms(set(str)): A collection of prediction terms
+
+    Returns:
+        prediction(str): in ['uncertain_significance','benign','likely_benign',
+                             'likely_oncogenic','oncogenic']
+
+    """
+    if not ccv_terms:
+        return None
+
+    points = get_ccv_points(ccv_terms)
+
+    if points <= -7:
+        prediction = "benign"
+    elif points <= -1:
+        prediction = "likely_benign"
+    elif points <= 5:
+        prediction = "uncertain_significance"
+    elif points <= 9:
+        prediction = "likely_oncogenic"
+    elif points >= 10:
+        prediction = "oncogenic"
+
+    return prediction
+
+
+def get_ccv_temperature(ccv_terms: set) -> Optional[dict]:
+    """
+    Use the algorithm described in Clingen-CGC-VIGG classification paper (Horak 2022)
+
+    O >= 10
+    OP 6 <= p <= 9
+    VUS 0 <= p <= 5
+    LB -1 <= p <= -6
+    B <= -7
+
+    If no terms return None
+
+    Args:
+        ccv_terms(set(str)): A collection of prediction terms
+
+    Returns:
+        dict:
+            temperature:
+        (points, temperature, point_classification)
+
+    """
+    TEMPERATURE_STRINGS = {
+        -1: {"label": "B/LB", "color": "success", "icon": "fa-times"},
+        0: {"label": "Ice cold", "color": "info", "icon": "fa-icicles"},
+        1: {"label": "Cold", "color": "info", "icon": "fa-snowman"},
+        2: {"label": "Cold", "color": "info", "icon": "fa-snowflake"},
+        3: {"label": "Tepid", "color": "yellow", "icon": "fa-temperature-half"},
+        4: {"label": "Warm", "color": "orange", "icon": "fa-mug-hot"},
+        5: {"label": "Hot", "color": "red", "icon": "fa-pepper-hot"},
+        6: {"label": "LO/O", "color": "danger", "icon": "fa-stethoscope"},
+    }
+
+    if not ccv_terms:
+        return {}
+
+    points = get_ccv_points(ccv_terms)
+
+    if points <= -7:
+        point_classification = "benign"
+        temperature_icon = TEMPERATURE_STRINGS[-1].get("icon")
+    elif points <= -1:
+        point_classification = "likely_benign"
+        temperature_icon = TEMPERATURE_STRINGS[-1].get("icon")
+    elif points <= 5:
+        point_classification = "uncertain_significance"
+    elif points <= 9:
+        point_classification = "likely_oncogenic"
+        temperature_icon = TEMPERATURE_STRINGS[6].get("icon")
+    elif points >= 10:
+        point_classification = "oncogenic"
+        temperature_icon = TEMPERATURE_STRINGS[6].get("icon")
+
+    temperature_class = CCV_COMPLETE_MAP[point_classification].get("color")
+    temperature = CCV_COMPLETE_MAP[point_classification].get("label")
+
+    if point_classification == "uncertain_significance":
+        temperature_class = TEMPERATURE_STRINGS[points].get("color")
+        temperature = TEMPERATURE_STRINGS[points].get("label")
+        temperature_icon = TEMPERATURE_STRINGS[points].get("icon")
+
+    return {
+        "points": points,
+        "temperature": temperature,
+        "temperature_class": temperature_class,
+        "temperature_icon": temperature_icon,
+        "point_classification": CCV_COMPLETE_MAP[point_classification].get("short"),
+    }
+
+
+def get_ccv_conflicts(ccv_terms: set) -> list:
+    """Check potential conflict paris, return list of reference strings."""
+
+    conflicts = []
+    for t1, t2, reference in CCV_POTENTIAL_CONFLICTS:
+        if t1 in ccv_terms and t2 in ccv_terms:
+            conflicts.append(reference)
+
+    return conflicts

scout/utils/link.py

@@ -36,15 +36,16 @@ def genes_by_alias(hgnc_genes):
         hgnc_symbol = gene["hgnc_symbol"]
 
         for alias in gene["previous_symbols"]:
+            alias = alias.upper()
             true_id = None
             if alias == hgnc_symbol:
                 true_id = hgnc_id
             if alias in alias_genes:
-                alias_genes[alias.upper()]["ids"].add(hgnc_id)
+                alias_genes[alias]["ids"].add(hgnc_id)
                 if true_id:
-                    alias_genes[alias.upper()]["true"] = hgnc_id
+                    alias_genes[alias]["true"] = hgnc_id
             else:
-                alias_genes[alias.upper()] = {"true": true_id, "ids": set([hgnc_id])}
+                alias_genes[alias] = {"true": true_id, "ids": set([hgnc_id])}
 
     return alias_genes
 

{scout_browser-4.92.dist-info → scout_browser-4.95.0.dist-info}/METADATA

@@ -1,61 +1,76 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.92
-Summary: Clinical DNA variant visualizer and browser.
-Home-page: https://github.com/Clinical-Genomics/scout
-Author: Måns Magnusson
-Author-email: mans.magnusson@scilifelab.se
+Version: 4.95.0
+Summary: Clinical DNA variant visualizer and browser
+Project-URL: Repository, https://github.com/Clinical-Genomics/scout
+Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
+Project-URL: Documentation, https://clinical-genomics.github.io/scout/
+Project-URL: Bug Tracker, https://github.com/Clinical-Genomics/scout/issues
+Project-URL: Issues, https://github.com/Clinical-Genomics/scout/issues
+Author-email: Chiara Rasi <chiara.rasi@scilifelab.se>, Daniel Nilsson <daniel.nilsson@ki.se>, Robin Andeer <robin.andeer@gmail.com>, Mans Magnuson <monsunas@gmail.com>
+License: MIT License
+License-File: LICENSE
+Keywords: acmg,beacon,cancer,clingen-cgc-vicc,clinvar,cnv,coverage,dna,fusion,genome visualisation,lrs,matchmaker exchange,ogm,outliers,panel,panelapp,phenopacket,rna,sma,snv,str,sv,variant ranking,variant triage,variants,vcf,wes,wgs,wts
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Web Environment
 Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Unix
 Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
-Classifier: Topic :: Software Development :: Libraries
-Classifier: Programming Language :: Python :: 3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: werkzeug
-Requires-Dist: Flask>=2.0
-Requires-Dist: Flask-Bootstrap
-Requires-Dist: Flask-CORS
-Requires-Dist: path.py
-Requires-Dist: markdown
-Requires-Dist: WTForms
-Requires-Dist: Flask-WTF
-Requires-Dist: Flask-Mail
-Requires-Dist: coloredlogs
-Requires-Dist: query-phenomizer
-Requires-Dist: Flask-Babel>=3
-Requires-Dist: livereload>=2.7
-Requires-Dist: tornado>=6.4.1
-Requires-Dist: python-dateutil
-Requires-Dist: pymongo
-Requires-Dist: pathlib
-Requires-Dist: pdfkit
-Requires-Dist: phenopackets
-Requires-Dist: xlsxwriter
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.9
+Requires-Dist: anytree
+Requires-Dist: authlib
+Requires-Dist: cairosvg
 Requires-Dist: click
+Requires-Dist: coloredlogs
+Requires-Dist: configobj
 Requires-Dist: cryptography
+Requires-Dist: cyvcf2
 Requires-Dist: defusedxml
-Requires-Dist: svglib
-Requires-Dist: cairosvg
-Requires-Dist: importlib-resources
-Requires-Dist: authlib
-Requires-Dist: flask-login
+Requires-Dist: flask-babel>=3
+Requires-Dist: flask-bootstrap
+Requires-Dist: flask-cors
 Requires-Dist: flask-ldapconn
-Requires-Dist: cyvcf2
-Requires-Dist: configobj
+Requires-Dist: flask-login
+Requires-Dist: flask-mail
+Requires-Dist: flask-wtf
+Requires-Dist: flask>=2.0
+Requires-Dist: importlib-resources
+Requires-Dist: intervaltree==3.0.2
+Requires-Dist: livereload>=2.7
+Requires-Dist: markdown
+Requires-Dist: path-py
+Requires-Dist: pathlib
+Requires-Dist: pdfkit
 Requires-Dist: ped-parser
+Requires-Dist: phenopackets
 Requires-Dist: pydantic>=2
-Requires-Dist: PyYaml>=5.1
-Requires-Dist: intervaltree==3.0.2
-Requires-Dist: anytree
+Requires-Dist: pymongo
+Requires-Dist: python-dateutil
+Requires-Dist: pyyaml>=5.1
+Requires-Dist: query-phenomizer
+Requires-Dist: svglib
 Requires-Dist: tabulate
+Requires-Dist: tornado>=6.4.1
+Requires-Dist: werkzeug
+Requires-Dist: wtforms
+Requires-Dist: xlsxwriter
 Provides-Extra: coverage
-Requires-Dist: chanjo-report; extra == "coverage"
-Requires-Dist: pymysql; extra == "coverage"
-
+Requires-Dist: chanjo-report; extra == 'coverage'
+Requires-Dist: pymysql; extra == 'coverage'
+Requires-Dist: python-dateutil; extra == 'coverage'
+Description-Content-Type: text/markdown
 
 <p align="center">
 	<a href="https://Clinical-Genomics.github.io/scout/">
@@ -126,6 +141,13 @@ cd scout
 pip install --editable .
 ```
 
+Scout is configured to use `uv` if you like; either run, install, install as a tool or
+```
+uv sync --frozen
+uv run scout
+```
+
+
 Scout PDF reports are created using [Flask-WeasyPrint](https://pythonhosted.org/Flask-WeasyPrint/). This library requires external dependencies which need be installed separately (namely Cairo and Pango). See platform-specific instructions for Linux, macOS and Windows available on the WeasyPrint installation [pages](https://doc.courtbouillon.org/weasyprint/stable/first_steps.html#installation).
 
 <b>NB</b>: in order to convert HTML reports into PDF reports, we have recently switched from the WeasyPrint lib to [python-pdfkit](https://github.com/JazzCore/python-pdfkit). For this reason, when upgrading to a Scout version >4.47, you need to install an additional [wkhtmltopdf system library](https://wkhtmltopdf.org/).