v2.1.0 (#76)

* Bump rich from 9.11.1 to 9.12.0

Bumps [rich](https://github.com/willmcgugan/rich) from 9.11.1 to 9.12.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v9.11.1...9.12.0)

Signed-off-by: dependabot[bot] <[email protected]>

* Fixed typo.

* Removed dependency shield

* Bump rich from 9.12.0 to 9.12.3

Bumps [rich](https://github.com/willmcgugan/rich) from 9.12.0 to 9.12.3.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@9.12.0...v9.12.3)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 9.12.3 to 9.12.4

Bumps [rich](https://github.com/willmcgugan/rich) from 9.12.3 to 9.12.4.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v9.12.3...v9.12.4)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump pandas from 1.2.2 to 1.2.3

Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.2.2 to 1.2.3.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md)
- [Commits](pandas-dev/pandas@v1.2.2...v1.2.3)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 9.12.4 to 9.13.0

Bumps [rich](https://github.com/willmcgugan/rich) from 9.12.4 to 9.13.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v9.12.4...v9.13.0)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 9.13.0 to 10.0.0

Bumps [rich](https://github.com/willmcgugan/rich) from 9.13.0 to 10.0.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v9.13.0...v10.0.0)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump matplotlib from 3.3.4 to 3.4.0

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.3.4 to 3.4.0.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.3.4...v3.4.0)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump numpy from 1.20.1 to 1.20.2

Bumps [numpy](https://github.com/numpy/numpy) from 1.20.1 to 1.20.2.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt)
- [Commits](numpy/numpy@v1.20.1...v1.20.2)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.0.0 to 10.0.1

Bumps [rich](https://github.com/willmcgugan/rich) from 10.0.0 to 10.0.1.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.0.0...v10.0.1)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump matplotlib from 3.4.0 to 3.4.1

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.4.0 to 3.4.1.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.4.0...v3.4.1)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump pytest from 6.2.2 to 6.2.3

Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.2 to 6.2.3.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@6.2.2...6.2.3)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.0.1 to 10.1.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.0.1 to 10.1.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.0.1...v10.1.0)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump pandas from 1.2.3 to 1.2.4

Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.2.3 to 1.2.4.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md)
- [Commits](pandas-dev/pandas@v1.2.3...v1.2.4)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump pytest from 6.2.3 to 6.2.4

Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.3 to 6.2.4.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@6.2.3...6.2.4)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.1.0 to 10.2.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.1.0 to 10.2.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.1.0...v10.2.0)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump numpy from 1.20.2 to 1.20.3

Bumps [numpy](https://github.com/numpy/numpy) from 1.20.2 to 1.20.3.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt)
- [Commits](numpy/numpy@v1.20.2...v1.20.3)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump matplotlib from 3.4.1 to 3.4.2

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.4.1 to 3.4.2.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.4.1...v3.4.2)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.2.0 to 10.2.2

Bumps [rich](https://github.com/willmcgugan/rich) from 10.2.0 to 10.2.2.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.2.0...v10.2.2)

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.2.2 to 10.3.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.2.2 to 10.3.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.2.2...v10.3.0)

---
updated-dependencies:
- dependency-name: rich
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.3.0 to 10.4.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.3.0 to 10.4.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.3.0...v10.4.0)

---
updated-dependencies:
- dependency-name: rich
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump pandas from 1.2.4 to 1.2.5

Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.2.4 to 1.2.5.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md)
- [Commits](pandas-dev/pandas@v1.2.4...v1.2.5)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump numpy from 1.20.3 to 1.21.0

Bumps [numpy](https://github.com/numpy/numpy) from 1.20.3 to 1.21.0.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt)
- [Commits](numpy/numpy@v1.20.3...v1.21.0)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Dropped Python3.6 action

* Dropped Python3.6 support.

* Bump rich from 10.4.0 to 10.5.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.4.0 to 10.5.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.4.0...v10.5.0)

---
updated-dependencies:
- dependency-name: rich
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.5.0 to 10.6.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.5.0 to 10.6.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.5.0...v10.6.0)

---
updated-dependencies:
- dependency-name: rich
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump numpy from 1.21.0 to 1.21.1

Bumps [numpy](https://github.com/numpy/numpy) from 1.21.0 to 1.21.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt)
- [Commits](numpy/numpy@v1.21.0...v1.21.1)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump pandas from 1.2.5 to 1.3.1

Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.2.5 to 1.3.1.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md)
- [Commits](pandas-dev/pandas@v1.2.5...v1.3.1)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.6.0 to 10.7.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.6.0 to 10.7.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.6.0...v10.7.0)

---
updated-dependencies:
- dependency-name: rich
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump matplotlib from 3.4.2 to 3.4.3

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.4.2 to 3.4.3.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.4.2...v3.4.3)

---
updated-dependencies:
- dependency-name: matplotlib
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump pandas from 1.3.1 to 1.3.2

Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.3.1 to 1.3.2.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md)
- [Commits](pandas-dev/pandas@v1.3.1...v1.3.2)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.7.0 to 10.9.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.7.0 to 10.9.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.7.0...v10.9.0)

---
updated-dependencies:
- dependency-name: rich
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump pytest from 6.2.4 to 6.2.5

Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.4 to 6.2.5.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@6.2.4...6.2.5)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Sourcery refactored dev branch (#70)

* 'Refactored by Sourcery'

* Blacked, flaked, and mypyed

Co-authored-by: Sourcery AI <>
Co-authored-by: Gabriele Girelli <[email protected]>

* Bump pandas from 1.3.2 to 1.3.3

Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.3.2 to 1.3.3.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md)
- [Commits](pandas-dev/pandas@v1.3.2...v1.3.3)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.9.0 to 10.10.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.9.0 to 10.10.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.9.0...v10.10.0)

---
updated-dependencies:
- dependency-name: rich
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.10.0 to 10.11.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.10.0 to 10.11.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.10.0...v10.11.0)

---
updated-dependencies:
- dependency-name: rich
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump rich from 10.11.0 to 10.12.0

Bumps [rich](https://github.com/willmcgugan/rich) from 10.11.0 to 10.12.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v10.11.0...v10.12.0)

---
updated-dependencies:
- dependency-name: rich
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump joblib from 1.0.1 to 1.1.0

Bumps [joblib](https://github.com/joblib/joblib) from 1.0.1 to 1.1.0.
- [Release notes](https://github.com/joblib/joblib/releases)
- [Changelog](https://github.com/joblib/joblib/blob/master/CHANGES.rst)
- [Commits](joblib/joblib@1.0.1...1.1.0)

---
updated-dependencies:
- dependency-name: joblib
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Added pre-commits and fixed typos.

* Fixed tab switch trigger and beautified HTML.

* fix: beautified.

* fix: import issues and alternative tab controls

* feat: increased version tag

* 'Refactored by Sourcery' (#77)

Co-authored-by: Sourcery AI <>

* feat: import with importlib for custom routes

* fix: switched to importlib.util

* fix: dependencies

* fix: added args for new routes

* fix: issue with pd app URL check

* v.2.1.0

* Fixed URLs

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>

.github/workflows/pythonpackage.yml

@@ -39,7 +39,7 @@ jobs:
       fail-fast: true
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.7, 3.8, 3.9]
     runs-on: ${{ matrix.os }}
     steps:
     # Checkout repo and setup python

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+default_language_version:
+    python: python3.8
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.0.1"
+    hooks:
+    -   id: check-added-large-files
+    -   id: check-ast
+    -   id: check-docstring-first
+    -   id: check-yaml
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v0.910-1"
+    hooks:
+    -   id: mypy
+-   repo: https://github.com/psf/black
+    rev: "21.9b0"
+    hooks:
+    -   id: black
+-   repo:  https://github.com/PyCQA/flake8
+    rev: "4.0.1"
+    hooks:
+    -   id: flake8
+        args: ["--count", "--select=E9,F63,F7,F82", "--show-source", "--statistics"]
+    -   id: flake8
+        args: ["--count", "--exit-zero", "--max-complexity=5", "--max-line-length=88", "--ignore=E203", "--statistics"]
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.1.0
+    hooks:
+    -   id: codespell
+        entry: codespell --ignore-words=ignore-spelling-words.txt
+        language: python
+        types: [text]

CHANGELOG.md

@@ -8,6 +8,19 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## Unreleased
 
+## [2.1.0] - 2021-10-20
+### Added
+- Pre-commit hooks.
+
+### Changed
+- Import of custom routes script with `importlib.util`.
+- Updated dependencies.
+- Dropped support for Python 3.6.
+
+### Fixed
+- Typo in GUI via `ifpd serve`.
+- Typos in GUI.
+- Alternative tab switcher of probe-design GUI.
 
 
 ## [2.0.5] - 2021-02-22
@@ -172,12 +185,18 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ## [0.0.1] - 2017-08-06 - First release
 
 
-
-[2.0.3.post2] https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.3.post2
-[2.0.3.post1] https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.3.post1
-[2.0.3] https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.3
-[2.0.2] https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.2
-[2.0.1] https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.1
-[2.0.0.post1] https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.0.post1
-[1.1.0] https://github.com/ggirelli/iFISH-Probe-Design/releases/tag/v1.1.0  
-[0.0.1] https://github.com/ggirelli/iFISH-Probe-Design/releases/tag/v0.0.1  
+[2.1.0]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.1.0
+[2.0.5]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.5
+[2.0.4]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.4
+[2.0.3.post2]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.3.post2
+[2.0.3.post1]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.3.post1
+[2.0.3]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.3
+[2.0.2]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.2
+[2.0.1.post6]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.1.post6
+[2.0.1.post5]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.1.post5
+[2.0.1.post4]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.1.post4
+[2.0.1.post3]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.1.post3
+[2.0.1]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.1
+[2.0.0.post1]: https://github.com/ggirelli/iFISH-probe-design/releases/tag/v2.0.0.post1
+[1.1.0]: https://github.com/ggirelli/iFISH-Probe-Design/releases/tag/v1.1.0  
+[0.0.1]: https://github.com/ggirelli/iFISH-Probe-Design/releases/tag/v0.0.1  

README.md

@@ -1,20 +1,20 @@
 # iFISH-Probe-Design
 
-[![DOI](https://zenodo.org/badge/143724120.svg)](https://zenodo.org/badge/latestdoi/143724120) ![](https://img.shields.io/librariesio/github/ggirelli/ifish-probe-design.svg?style=flat) ![](https://img.shields.io/github/license/ggirelli/ifish-probe-design.svg?style=flat)  
+[![DOI](https://zenodo.org/badge/143724120.svg)](https://zenodo.org/badge/latestdoi/143724120) ![](https://img.shields.io/github/license/ggirelli/ifish-probe-design.svg?style=flat)  
 ![](https://github.com/ggirelli/ifish-probe-design/workflows/Python%20package/badge.svg?branch=main&event=push) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/ifpd) ![PyPI - Format](https://img.shields.io/pypi/format/ifpd) ![PyPI - Status](https://img.shields.io/pypi/status/ifpd)  
 ![](https://img.shields.io/github/release/ggirelli/ifish-probe-design.svg?style=flat) ![](https://img.shields.io/github/release-date/ggirelli/ifish-probe-design.svg?style=flat) ![](https://img.shields.io/github/languages/code-size/ggirelli/ifish-probe-design.svg?style=flat)  
 ![](https://img.shields.io/github/watchers/ggirelli/ifish-probe-design.svg?label=Watch&style=social) ![](https://img.shields.io/github/stars/ggirelli/ifish-probe-design.svg?style=social)
 
 [PyPi](https://pypi.org/project/ifpd/) | [docs](https://ggirelli.github.io/iFISH-probe-design/)
 
 
-**iFISH-Probe-Design** (`ifpd`) is a Python3.6.1+ package containing tools for selection of complementary oligonucleotides to build iFISH probes. It also includes a web interface, which simplifies the procedure by removing any requirement for programming skills. Read the online [documentation](https://ggirelli.github.io/iFISH-probe-design/) for more details.
+**iFISH-Probe-Design** (`ifpd`) is a Python3.7+ package containing tools for selection of complementary oligonucleotides to build iFISH probes. It also includes a web interface, which simplifies the procedure by removing any requirement for programming skills. Read the online [documentation](https://ggirelli.github.io/iFISH-probe-design/) for more details.
 
 ## Requirements
 
-**iFISH-Probe-Designer** is fully implemented in Python3.6.1+, thus you need Python3 to run it. Check out [here](https://realpython.com/installing-python/) how to install Python3.6.1+ on your machine if you don't have it yet.
+**iFISH-Probe-Designer** is fully implemented in Python3.7+, thus you need Python3 to run it. Check out [here](https://realpython.com/installing-python/) how to install Python3.7+ on your machine if you don't have it yet.
 
-`ifpd` has been tested with Python 3.6.1, 3.7, and 3.8. We recommend installing it using `pipx` (see [below](https://github.com/ggirelli/ifish-probe-design#install)) to avoid dependency conflicts with other packages. The packages it depends on are listed in our [dependency graph](https://github.com/ggirelli/ifish-probe-design/network/dependencies). We use [`poetry`](https://github.com/python-poetry/poetry) to handle our dependencies.
+`ifpd` has been tested with Python 3.7, 3.8, and 3.9. We recommend installing it using `pipx` (see [below](https://github.com/ggirelli/ifish-probe-design#install)) to avoid dependency conflicts with other packages. The packages it depends on are listed in our [dependency graph](https://github.com/ggirelli/ifish-probe-design/network/dependencies). We use [`poetry`](https://github.com/python-poetry/poetry) to handle our dependencies.
 
 ## Installation
 
@@ -32,7 +32,7 @@ We welcome any contributions to `ifpd`. In short, we use [`black`](https://githu
 
 ### Reference
 
-* Gelali, E., Girelli, G., Matsumoto, M., Wernersson, E., Custodio, J., Mota, A., ... & Bienko, M. (2019). iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture. Nature communications, 10(1), 1-15. ([link](https://www.nature.com/articles/s41467-019-09616-w))
+* Gelali, E., Girelli, G., Matsumoto, M., Wernersson, E., Custodio, J., Mota, A., ... & Bienko, M. (2019). iFISH is a publicly available resource enabling versatile DNA FISH to study genome architecture. Nature communications, 10(1), 1-15. ([link](https://www.nature.com/articles/s41467-019-09616-w))
 
 ## License
 

docs/index.md

@@ -13,4 +13,4 @@ The tools allow to select sets of oligomers as iFISH probes, starting from datab
 
 ### Reference
 
-Gelali, E., Girelli, G., Matsumoto, M., Wernersson, E., Custodio, J., Mota, A., ... & Bienko, M. (2019). iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture. Nature communications, 10(1), 1-15. ([link](https://www.nature.com/articles/s41467-019-09616-w))
+Gelali, E., Girelli, G., Matsumoto, M., Wernersson, E., Custodio, J., Mota, A., ... & Bienko, M. (2019). iFISH is a publicly available resource enabling versatile DNA FISH to study genome architecture. Nature communications, 10(1), 1-15. ([link](https://www.nature.com/articles/s41467-019-09616-w))

docs/interface.md

@@ -13,8 +13,8 @@ The interface is fully responsive, and can be visualized with a display of any s
 <!-- MarkdownTOC -->
 
 - [Homepage](#homepage)
-    - [Single probe](#single-probe)
-    - [Spotting probe](#spotting-probe)
+  - [Single probe](#single-probe)
+  - [Spotting probe](#spotting-probe)
 - [Query page](#query-page)
 - [Probe candidate page](#probe-candidate-page)
 - [Probe set candidate page](#probe-set-candidate-page)
@@ -88,7 +88,7 @@ When the query leaves the queue, the <span class="text-warning">yellow</span> al
 ![query-head-success]({{ site.baseurl }}/images/query-head-success.png)
 ![query-head-timeout]({{ site.baseurl }}/images/query-head-timeout.png)
 
-Once the query is processed, the alert turns <span class="text-success">green</span> and reports the time at which the query was completed, alongside the running time. If something wrong happend during the processing, or if the query took too long, the alert turns <span class="text-dange">red</span> and invites the user to try again or contact the server admin.
+Once the query is processed, the alert turns <span class="text-success">green</span> and reports the time at which the query was completed, alongside the running time. If something wrong happened during the processing, or if the query took too long, the alert turns <span class="text-dange">red</span> and invites the user to try again or contact the server admin.
 
 ![query-head-info]({{ site.baseurl }}/images/query-head-info.png)
 

docs/introduction.md

@@ -4,7 +4,7 @@ title: Introduction to ifpd
 
 The `ifpd` package aims to simplify the design of fluorescence *in situ* hybridization probes, starting from [databases]({{ site.baseurl }}/database) of oligonucleotides designed to *specifically* bind to genomic loci of interest.
 
-The package contains tools to design a single probe, comprising a specific number of oligonucleotide sequences. Alternatively, it also allows to design anumber of homogeneously spread probes, covering a region of interest, in a fashion that we dubbed *spotting* probe. More details on these two [algorithms]({{ site.baseurl }}/algorithms) are available in the relative page.
+The package contains tools to design a single probe, comprising a specific number of oligonucleotide sequences. Alternatively, it also allows to design a number of homogeneously spread probes, covering a region of interest, in a fashion that we dubbed *spotting* probe. More details on these two [algorithms]({{ site.baseurl }}/algorithms) are available in the relative page.
 
 `ifpd` is fully implemented in Python3, and is distributed through the PyPI network: the Python Package Manager developed and maintained by the Python community, for the Python community.
 

ifpd/query.py

@@ -98,7 +98,7 @@ def read_chromosome(self, chrom):
         oligoMinDist = self.get_oligo_min_dist()
         startValues = chromData.iloc[1:, 0].values
         endValues = chromData.iloc[:-1, 1].values
-        if 0 != len(startValues):
+        if len(startValues) != 0:
             oligoMinD_observed = min(startValues - endValues)
         else:
             oligoMinD_observed = np.inf
@@ -189,10 +189,9 @@ def get_probe_centrality(self, region):
         at either of the region extremities."""
         region_halfWidth = (region[2] - region[1]) / 2
         region_midPoint = region[1] + region_halfWidth
-        centrality = (
+        return (
             region_halfWidth - abs(region_midPoint - self.midpoint)
         ) / region_halfWidth
-        return centrality
 
     def get_probe_size(self):
         """Probe size, defined as difference between start of first oligo
@@ -204,7 +203,7 @@ def get_probe_homogeneity(self):
         distance between consecutive oligos, calculated from their start
         position, disregarding oligo length."""
         std = np.std(np.diff(self.oligoData.iloc[:, 1]))
-        return np.inf if 0 == std else 1 / std
+        return np.inf if std == 0 else 1 / std
 
     def describe(self, region, path=None):
         """Builds a small pd.DataFrame describing a probe."""
@@ -219,7 +218,7 @@ def describe(self, region, path=None):
             }
         )
 
-        if not type(None) == type(path):
+        if type(None) != type(path):
             config = configparser.ConfigParser()
             config["REGION"] = {
                 "chrom": region[0],
@@ -254,7 +253,7 @@ def get_fasta(self, path=None, prefix=""):
             fasta += f"{self.chrom}:{chromStart}-{chromEnd}\n"
             fasta += f"{sequence}\n"
 
-        if not type(None) == type(path):
+        if type(None) != type(path):
             assert os.path.isdir(os.path.dirname(path))
             with open(path, "w+") as OH:
                 OH.write(fasta)
@@ -272,7 +271,7 @@ def get_bed(self, path=None, prefix=""):
             bed += f"{self.chrom}\t{chromStart}\t{chromEnd}\t"
             bed += f"{prefix}oligo_{i}\n"
 
-        if not type(None) == type(path):
+        if type(None) != type(path):
             assert os.path.isdir(os.path.dirname(path))
             with open(path, "w+") as OH:
                 OH.write(bed)
@@ -387,7 +386,7 @@ def _plot_oligo_distr(self, outputDir):
     def _plot_oligo_distance(self, outputDir):
         fig = plt.figure()
 
-        if 1 < self.oligoData.shape[0]:
+        if self.oligoData.shape[0] > 1:
             startPositions = self.oligoData.iloc[1:, 0].values
             endPositions = self.oligoData.iloc[:-1, 1].values
             diffs = startPositions - endPositions
@@ -433,7 +432,7 @@ def __init__(self, candidateList, queried_region, verbose=False, threads=1):
         assert 0 < len(candidateList)
 
         self.data = []
-        if 1 != threads:
+        if threads != 1:
             verbose = 1 if verbose else 0
             self.data = Parallel(n_jobs=threads, backend="threading", verbose=verbose)(
                 delayed(describe_candidate)(candidate, queried_region)
@@ -475,8 +474,11 @@ def filter(self, feature, thr, cumulative=False):
         feature_delta = best_feature * thr
         feature_range = (best_feature - feature_delta, best_feature + feature_delta)
 
-        discardCondition = [self.data[feature] < feature_range[0]]
-        discardCondition.append(self.data[feature] > feature_range[1])
+        discardCondition = [
+            self.data[feature] < feature_range[0],
+            self.data[feature] > feature_range[1],
+        ]
+
         discardCondition = np.logical_or(*discardCondition)
         self.discarded = pd.concat([self.discarded, self.data.loc[discardCondition, :]])
         self.data = self.data.loc[np.logical_not(discardCondition), :]
@@ -531,8 +533,7 @@ def __getitem__(self, i):
         return self.data[i]
 
     def __iter__(self):
-        for window in self.data:
-            yield window
+        yield from self.data
 
     def __len__(self):
         return len(self.data)
@@ -541,7 +542,7 @@ def add(self, chrom, start, size):
         self.data.append(GenomicWindow(chrom, start, size))
 
     def count_probes(self):
-        return sum([w.has_probe() for w in self])
+        return sum(w.has_probe() for w in self)
 
     def shift(self, n):
         return GenomicWindowList([window.shift(n) for window in self.data])
@@ -551,7 +552,7 @@ def sort(self):
         self.data = [self.data[i] for i in np.argsort(midpointList)]
 
     def calc_probe_size_and_homogeneity(self):
-        if 3 > self.count_probes():
+        if self.count_probes() < 3:
             return np.nan
 
         probeData = pd.concat(
@@ -651,7 +652,7 @@ def _plot_probe_distr(self, outputDir):
 
         probes = [w.probe for w in self if w.probe is not None]
 
-        if 1 < len(probes):
+        if len(probes) > 1:
             plt.plot(
                 [0, len(probes) - 1],
                 [probes[0].midpoint, probes[-1].midpoint],
@@ -684,7 +685,7 @@ def _plot_probe_distance(self, outputDir, region):
 
         probes = [w.probe for w in self if w.probe is not None]
 
-        if 1 < len(probes):
+        if len(probes) > 1:
             starts = np.array([p.chromStart for p in probes][1:])
             ends = np.array([p.chromEnd for p in probes][:-1])
             diffs = starts - ends

ifpd/scripts/arguments.py

@@ -69,7 +69,7 @@ def add_log_file_handler(path: str, logger_name: Optional[str] = None) -> None:
     """
     assert not os.path.isdir(path)
     log_dir = os.path.dirname(path)
-    assert os.path.isdir(log_dir) or "" == log_dir
+    assert os.path.isdir(log_dir) or log_dir == ""
     fh = RichHandler(console=Console(file=open(path, mode="w+")), markup=True)
     fh.setLevel(logging.INFO)
     logging.getLogger(logger_name).addHandler(fh)

ifpd/scripts/mkdb.py

@@ -111,7 +111,7 @@ def init_parser(subparsers: argparse._SubParsersAction) -> argparse.ArgumentPars
 
 @enable_rich_assert
 def parse_arguments(args: argparse.Namespace) -> argparse.Namespace:
-    if "." == args.output:
+    if args.output == ".":
         args.output = args.dbName
 
     assert os.path.isfile(args.input), f'input file not found: "{args.input}"'
@@ -123,7 +123,6 @@ def parse_arguments(args: argparse.Namespace) -> argparse.Namespace:
         if os.path.isdir(args.output):
             logging.warning("'-f' option used. Removing previously generated database.")
             shutil.rmtree(args.output)
-            pass
     else:
         assert not os.path.isdir(
             args.output
@@ -155,7 +154,7 @@ def sort_oligos(args, chromList):
         oligoLengthRange[1] = max(oligoLengthRange[1], oligoLengthList.max())
 
         assert len(startPositions) == len(endPositions)
-        if 0 == len(startPositions):
+        if len(startPositions) == 0:
             continue
         oligoMinDist = min(oligoMinDist, min(startPositions - endPositions - 1))
     return oligoMinDist, oligoLengthRange, has_overlaps
@@ -199,7 +198,7 @@ def run(args: argparse.Namespace) -> None:
     logging.info("Parse and write database.")
     chromList = set()
     for line in oligoGenerator:
-        if 0 == len(line.strip()):
+        if len(line.strip()) == 0:
             continue
         line = line.strip().split("\t")
         chrom = line.pop(0)

ifpd/scripts/query/probe.py

@@ -177,7 +177,7 @@ def parse_arguments(args: argparse.Namespace) -> argparse.Namespace:
         ), f'unrecognized feature "{o}". Should be one of {const.featureList}.'
 
     assert (
-        0 <= args.filter_thr and 1 >= args.filter_thr
+        args.filter_thr >= 0 and args.filter_thr <= 1
     ), "first filter threshold must be a fraction: {args.filter_thr}"
 
     assert (
@@ -222,17 +222,18 @@ def run(args: argparse.Namespace) -> None:
     args = ap.check_n_oligo(args, selectCondition)
 
     logging.info("Build probe candidates.")
-    candidateList = []
-    for i in track(
-        range(0, selectedOligos.shape[0] - args.n_oligo + 1), description="Building"
-    ):
-        candidateList.append(
-            query.OligoProbe(
-                queried_region[0],
-                selectedOligos.iloc[i : (i + args.n_oligo), :],
-                oligoDB,
-            )
+    candidateList = [
+        query.OligoProbe(
+            queried_region[0],
+            selectedOligos.iloc[i : (i + args.n_oligo), :],
+            oligoDB,
         )
+        for i in track(
+            range(selectedOligos.shape[0] - args.n_oligo + 1),
+            description="Building",
+        )
+    ]
+
     logging.info(f"Found {len(candidateList)} probe candidates.")
 
     logging.info("Describing candidates...")