Commit 1270bdb5 authored by Kruyff,D.L.W. (Dylan)'s avatar Kruyff,D.L.W. (Dylan)
Browse files

Install packages using environment.yml


Former-commit-id: 76231559
parent ba4a9f96

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.
......@@ -18,7 +18,7 @@ export class CacheService {
private _queryWindow;
public windowSize = 120;
public nrOfTables = 50;
public nrOfTables = 20;
public hashSize = 4;
public stepSize = 200;
public querySelectionMode = true;
......
......@@ -105,17 +105,17 @@ export class TableOverviewComponent implements OnInit {
return this.distanceMetric(hash1) - this.distanceMetric(hash2);
});
if (this.service.queryWindow) {
const queryEntry = this.calculateSignature(table.hash, this.service.queryWindow);
listOfWindows.push(table.entries[queryEntry]);
opacity = orderedHashes.map((hash: string) => {
return hash === queryEntry ? 1.0 : 0.5;
}
);
rank = table.entries[queryEntry].length;
// const queryEntry = this.calculateSignature(table.hash, this.service.queryWindow);
// listOfWindows.push(table.entries[queryEntry]);
// opacity = orderedHashes.map((hash: string) => {
// return hash === queryEntry ? 1.0 : 0.5;
// }
// );
// rank = table.entries[queryEntry].length;
}
this.subplots.push(
{
rank: rank,
// rank: rank,
data: [{
x: orderedHashes.map((hash: string, i) => {
return i; // Number('0b' + hash);
......@@ -149,7 +149,7 @@ export class TableOverviewComponent implements OnInit {
}
);
}
this.subplots.sort((plot1, plot2) => plot1.rank - plot2.rank);
// this.subplots.sort((plot1, plot2) => plot1.rank - plot2.rank);
if (this.service.queryWindow) {
const temp = await this.service.getAverageTableWindows(listOfWindows);
this.averages = temp.map(x => this.averagePlot(x));
......
......@@ -21,12 +21,8 @@
<component name="ChangeListManager">
<list default="true" id="556080ba-825c-4b55-a92a-867a4df4fb32" name="Default Changelist" comment="">
<change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/cache.service.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/cache.service.ts" afterDir="false" />
<change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/labeling-window/labeling-window.component.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/labeling-window/labeling-window.component.ts" afterDir="false" />
<change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/overview-window/overview-window.component.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/overview-window/overview-window.component.ts" afterDir="false" />
<change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/progress-view/progress-view.component.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/progress-view/progress-view.component.ts" afterDir="false" />
<change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
<change beforePath="$PROJECT_DIR$/main.py" beforeDir="false" afterPath="$PROJECT_DIR$/main.py" afterDir="false" />
<change beforePath="$PROJECT_DIR$/processed-data.npy" beforeDir="false" afterPath="$PROJECT_DIR$/processed-data.npy" afterDir="false" />
</list>
<option name="SHOW_DIALOG" value="false" />
<option name="HIGHLIGHT_CONFLICTS" value="true" />
......
......@@ -40,14 +40,13 @@ def read_data():
def create_windows():
t0 = time()
if reload:
size = bbi.chromsizes('test.bigWig')['chr1']
raw_data = request.json
window_size = int(raw_data['parameters']["windowsize"])
data = bigwig.chunk(
'test.bigWig',
12000,
12000 / window_size,
12000 / 6,
int(12000 / window_size),
int(12000 / 6),
['chr1'],
verbose=True,
)
......@@ -59,16 +58,12 @@ def create_windows():
@app.route('/create-tables', methods=['POST'])
def create_tables():
t0 = time()
print("loading")
data = np.load('processed-data.npy')
print('Number of tables: ' + str(data.shape))
print(time()-t0)
raw_data = orjson.loads(request.data)
print(time()-t0)
window_size = int(raw_data['parameters']["windowsize"])
hash_size = int(raw_data['parameters']["hashsize"])
table_size = int(raw_data['parameters']["tablesize"])
data = np.array(data)
print('Starting: ' + str(time()-t0))
tables_hash_function = [np.random.uniform(-100, 100, size=(window_size, hash_size)) for _ in range(table_size)]
print('Init time: ' + str(time() - t0))
......
Copyright 2010 Pallets
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Metadata-Version: 2.1
Name: Flask
Version: 1.1.2
Summary: A simple framework for building complex web applications.
Home-page: https://palletsprojects.com/p/flask/
Author: Armin Ronacher
Author-email: armin.ronacher@active-4.com
Maintainer: Pallets
Maintainer-email: contact@palletsprojects.com
License: BSD-3-Clause
Project-URL: Documentation, https://flask.palletsprojects.com/
Project-URL: Code, https://github.com/pallets/flask
Project-URL: Issue tracker, https://github.com/pallets/flask/issues
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Web Environment
Classifier: Framework :: Flask
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
Classifier: Topic :: Internet :: WWW/HTTP :: WSGI :: Application
Classifier: Topic :: Software Development :: Libraries :: Application Frameworks
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*
Requires-Dist: Werkzeug (>=0.15)
Requires-Dist: Jinja2 (>=2.10.1)
Requires-Dist: itsdangerous (>=0.24)
Requires-Dist: click (>=5.1)
Provides-Extra: dev
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: coverage ; extra == 'dev'
Requires-Dist: tox ; extra == 'dev'
Requires-Dist: sphinx ; extra == 'dev'
Requires-Dist: pallets-sphinx-themes ; extra == 'dev'
Requires-Dist: sphinxcontrib-log-cabinet ; extra == 'dev'
Requires-Dist: sphinx-issues ; extra == 'dev'
Provides-Extra: docs
Requires-Dist: sphinx ; extra == 'docs'
Requires-Dist: pallets-sphinx-themes ; extra == 'docs'
Requires-Dist: sphinxcontrib-log-cabinet ; extra == 'docs'
Requires-Dist: sphinx-issues ; extra == 'docs'
Provides-Extra: dotenv
Requires-Dist: python-dotenv ; extra == 'dotenv'
Flask
=====
Flask is a lightweight `WSGI`_ web application framework. It is designed
to make getting started quick and easy, with the ability to scale up to
complex applications. It began as a simple wrapper around `Werkzeug`_
and `Jinja`_ and has become one of the most popular Python web
application frameworks.
Flask offers suggestions, but doesn't enforce any dependencies or
project layout. It is up to the developer to choose the tools and
libraries they want to use. There are many extensions provided by the
community that make adding new functionality easy.
Installing
----------
Install and update using `pip`_:
.. code-block:: text
pip install -U Flask
A Simple Example
----------------
.. code-block:: python
from flask import Flask
app = Flask(__name__)
@app.route("/")
def hello():
return "Hello, World!"
.. code-block:: text
$ env FLASK_APP=hello.py flask run
* Serving Flask app "hello"
* Running on http://127.0.0.1:5000/ (Press CTRL+C to quit)
Contributing
------------
For guidance on setting up a development environment and how to make a
contribution to Flask, see the `contributing guidelines`_.
.. _contributing guidelines: https://github.com/pallets/flask/blob/master/CONTRIBUTING.rst
Donate
------
The Pallets organization develops and supports Flask and the libraries
it uses. In order to grow the community of contributors and users, and
allow the maintainers to devote more time to the projects, `please
donate today`_.
.. _please donate today: https://psfmember.org/civicrm/contribute/transact?reset=1&id=20
Links
-----
* Website: https://palletsprojects.com/p/flask/
* Documentation: https://flask.palletsprojects.com/
* Releases: https://pypi.org/project/Flask/
* Code: https://github.com/pallets/flask
* Issue tracker: https://github.com/pallets/flask/issues
* Test status: https://dev.azure.com/pallets/flask/_build
* Official chat: https://discord.gg/t6rrQZH
.. _WSGI: https://wsgi.readthedocs.io
.. _Werkzeug: https://www.palletsprojects.com/p/werkzeug/
.. _Jinja: https://www.palletsprojects.com/p/jinja/
.. _pip: https://pip.pypa.io/en/stable/quickstart/
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Wheel-Version: 1.0
Generator: bdist_wheel (0.33.6)
Root-Is-Purelib: true
Tag: py2-none-any
Tag: py3-none-any
Copyright 2007 Pallets
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Metadata-Version: 2.1
Name: Jinja2
Version: 2.11.2
Summary: A very fast and expressive template engine.
Home-page: https://palletsprojects.com/p/jinja/
Author: Armin Ronacher
Author-email: armin.ronacher@active-4.com
Maintainer: Pallets
Maintainer-email: contact@palletsprojects.com
License: BSD-3-Clause
Project-URL: Documentation, https://jinja.palletsprojects.com/
Project-URL: Code, https://github.com/pallets/jinja
Project-URL: Issue tracker, https://github.com/pallets/jinja/issues
Platform: UNKNOWN
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: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Text Processing :: Markup :: HTML
Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*
Description-Content-Type: text/x-rst
Requires-Dist: MarkupSafe (>=0.23)
Provides-Extra: i18n
Requires-Dist: Babel (>=0.8) ; extra == 'i18n'
Jinja
=====
Jinja is a fast, expressive, extensible templating engine. Special
placeholders in the template allow writing code similar to Python
syntax. Then the template is passed data to render the final document.
It includes:
- Template inheritance and inclusion.
- Define and import macros within templates.
- HTML templates can use autoescaping to prevent XSS from untrusted
user input.
- A sandboxed environment can safely render untrusted templates.
- AsyncIO support for generating templates and calling async
functions.
- I18N support with Babel.
- Templates are compiled to optimized Python code just-in-time and
cached, or can be compiled ahead-of-time.
- Exceptions point to the correct line in templates to make debugging
easier.
- Extensible filters, tests, functions, and even syntax.
Jinja's philosophy is that while application logic belongs in Python if
possible, it shouldn't make the template designer's job difficult by
restricting functionality too much.
Installing
----------
Install and update using `pip`_:
.. code-block:: text
$ pip install -U Jinja2
.. _pip: https://pip.pypa.io/en/stable/quickstart/
In A Nutshell
-------------
.. code-block:: jinja
{% extends "base.html" %}
{% block title %}Members{% endblock %}
{% block content %}
<ul>
{% for user in users %}
<li><a href="{{ user.url }}">{{ user.username }}</a></li>
{% endfor %}
</ul>
{% endblock %}
Links
-----
- Website: https://palletsprojects.com/p/jinja/
- Documentation: https://jinja.palletsprojects.com/
- Releases: https://pypi.org/project/Jinja2/
- Code: https://github.com/pallets/jinja
- Issue tracker: https://github.com/pallets/jinja/issues
- Test status: https://dev.azure.com/pallets/jinja/_build
- Official chat: https://discord.gg/t6rrQZH
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jinja2/filters.py,sha256=_RpPgAlgIj7ExvyDzcHAC3B36cocfWK-1TEketbNeM0,41415
jinja2/idtracking.py,sha256=J3O4VHsrbf3wzwiBc7Cro26kHb6_5kbULeIOzocchIU,9211
jinja2/lexer.py,sha256=nUFLRKhhKmmEWkLI65nQePgcQs7qsRdjVYZETMt_v0g,30331
jinja2/loaders.py,sha256=C-fST_dmFjgWkp0ZuCkrgICAoOsoSIF28wfAFink0oU,17666
jinja2/meta.py,sha256=QjyYhfNRD3QCXjBJpiPl9KgkEkGXJbAkCUq4-Ur10EQ,4131
jinja2/nativetypes.py,sha256=Ul__gtVw4xH-0qvUvnCNHedQeNDwmEuyLJztzzSPeRg,2753
jinja2/nodes.py,sha256=Mk1oJPVgIjnQw9WOqILvcu3rLepcFZ0ahxQm2mbwDwc,31095
jinja2/optimizer.py,sha256=gQLlMYzvQhluhzmAIFA1tXS0cwgWYOjprN-gTRcHVsc,1457
jinja2/parser.py,sha256=fcfdqePNTNyvosIvczbytVA332qpsURvYnCGcjDHSkA,35660
jinja2/runtime.py,sha256=0y-BRyIEZ9ltByL2Id6GpHe1oDRQAwNeQvI0SKobNMw,30618
jinja2/sandbox.py,sha256=knayyUvXsZ-F0mk15mO2-ehK9gsw04UhB8td-iUOtLc,17127
jinja2/tests.py,sha256=iO_Y-9Vo60zrVe1lMpSl5sKHqAxe2leZHC08OoZ8K24,4799
jinja2/utils.py,sha256=OoVMlQe9S2-lWT6jJbTu9tDuDvGNyWUhHDcE51i5_Do,22522
jinja2/visitor.py,sha256=DUHupl0a4PGp7nxRtZFttUzAi1ccxzqc2hzetPYUz8U,3240
Wheel-Version: 1.0
Generator: bdist_wheel (0.34.2)
Root-Is-Purelib: true
Tag: py2-none-any
Tag: py3-none-any
[babel.extractors]
jinja2 = jinja2.ext:babel_extract [i18n]
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