Merged in refactor/pre-commit (pull request #156)

Pre-commit 🤯

Approved-by: Randy Taylor

.bumpversion.cfg

@@ -1,7 +1,7 @@
 [bumpversion]
 current_version = 3.8.0
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
-serialize = 
+serialize =
 	{major}.{minor}.{patch}
 commit = False
 tag = False

.dockerignore

@@ -247,4 +247,3 @@ $RECYCLE.BIN/
 
 # Windows shortcuts
 *.lnk
-

.git-blame-ignore-revs

@@ -0,0 +1,5 @@
+6ad28467153aab333eba6fe65298904d836aa712
+778533215c89743e041303e10a79166187d0408b
+b21e47d612bc442204177ca492e444c31e923d75
+8ac3292a50e1aa8373bc01d897209514d67bb835
+b51cc243b0fb1ff301e4a24361b007ed54294800

.github/workflows/pypi_upload.yml

@@ -2,7 +2,7 @@
 
 name: PYPI_Upload
 
-# Controls when the action will run. 
+# Controls when the action will run.
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
   push:

.github/workflows/python-publish.yml

@@ -6,7 +6,7 @@ name: Upload Python Package
 on:
   release:
     types: [created]
-    
+
   workflow_dispatch:
 
 jobs:

.gitignore

@@ -4,6 +4,11 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# Pants tooling
+/.pants.*
+/dist/
+/.pids
+
 # C extensions
 *.so
 
@@ -110,6 +115,7 @@ celerybeat.pid
 .venv
 env/
 venv/
+venv310/
 ENV/
 env.bak/
 venv.bak/
@@ -236,4 +242,3 @@ $RECYCLE.BIN/
 
 # Windows shortcuts
 *.lnk
-

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: check-json
+    -   id: check-ast
+    -   id: check-yaml
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: requirements-txt-fixer
+    -   id: no-commit-to-branch
+        args: [--branch, master, --branch, staging, --branch, production]
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+    -   id: isort
+        args: ["--profile", "black", "--filter-files"]
+-   repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v3.3.1
+    hooks:
+    -   id: pyupgrade
+        args: [--py36-plus]
+-   repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+    -   id: flake8
+        stages:
+            - manual
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.991
+    hooks:
+    -   id: mypy
+        exclude: docs\*
+        stages:
+          - manual

LICENSE.txt

@@ -12,4 +12,4 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
-IN THE SOFTWARE.
+IN THE SOFTWARE.

MANIFEST.in

@@ -1 +1 @@
-prune tests*
+prune tests*

docs/source/calibration_docs.rst

@@ -305,4 +305,3 @@ TRS-398 API Documentation
 .. autoclass:: pylinac.calibration.trs398.TRS398Photon
 
 .. autoclass:: pylinac.calibration.trs398.TRS398Electron
-

docs/source/code_snippets/tg51_class.py

@@ -1,28 +1,33 @@
 """A script to calculate TG-51 dose using pylinac classes and following the TG-51 photon form"""
 from pylinac.calibration import tg51
 
-
 ENERGY = 6
 TEMP = 22.1
 PRESS = tg51.mmHg2kPa(755.0)
-CHAMBER = '30013'  # PTW
+CHAMBER = "30013"  # PTW
 P_ELEC = 1.000
 ND_w = 5.443  # Gy/nC
 MU = 200
 CLINICAL_PDD = 66.5
 
 tg51_6x = tg51.TG51Photon(
-    unit='TrueBeam1',
+    unit="TrueBeam1",
     chamber=CHAMBER,
-    temp=TEMP, press=PRESS,
-    n_dw=ND_w, p_elec=P_ELEC,
-    measured_pdd10=66.4, lead_foil=None,
-    clinical_pdd10=66.5, energy=ENERGY,
-    voltage_reference=-300, voltage_reduced=-150,
+    temp=TEMP,
+    press=PRESS,
+    n_dw=ND_w,
+    p_elec=P_ELEC,
+    measured_pdd10=66.4,
+    lead_foil=None,
+    clinical_pdd10=66.5,
+    energy=ENERGY,
+    voltage_reference=-300,
+    voltage_reduced=-150,
     m_reference=(25.65, 25.66, 25.65),
     m_opposite=(25.64, 25.65, 25.65),
     m_reduced=(25.64, 25.63, 25.63),
-    mu=MU, tissue_correction=1.0
+    mu=MU,
+    tissue_correction=1.0,
 )
 
 # Done!
@@ -39,4 +44,8 @@
 print(tg51_6x.dose_mu_dmax_adjusted)
 
 # generate a PDF for record-keeping
-tg51_6x.publish_pdf('TB1 6MV TG-51.pdf', notes=['My notes', 'I used Pylinac to do this; so easy!'], open_file=False)
+tg51_6x.publish_pdf(
+    "TB1 6MV TG-51.pdf",
+    notes=["My notes", "I used Pylinac to do this; so easy!"],
+    open_file=False,
+)

docs/source/code_snippets/tg51_function.py

@@ -1,11 +1,10 @@
 """A script to calculate TG-51 dose using pylinac functions and following the TG-51 photon form"""
 from pylinac.calibration import tg51
 
-
 ENERGY = 6
 TEMP = 22.1
 PRESS = tg51.mmHg2kPa(755.0)
-CHAMBER = '30013'  # PTW
+CHAMBER = "30013"  # PTW
 P_ELEC = 1.000
 ND_w = 5.443  # Gy/nC
 MU = 200
@@ -18,7 +17,7 @@
 # Section 5 (kQ)
 kq = tg51.kq_photon_pddx(chamber=CHAMBER, pddx=pdd10x)
 # Alternatively, get kQ from TPR (way quicker to measure, without needing to measure TPR!)
-tpr = tg51.tpr2010_from_pdd2010(pdd2010=(38.0/66.4))
+tpr = tg51.tpr2010_from_pdd2010(pdd2010=(38.0 / 66.4))
 kq = tg51.kq_photon_tpr(chamber=CHAMBER, tpr=tpr)
 
 # Section 6 (Temp/Press)
@@ -31,13 +30,20 @@
 
 # Section 8 (ionization)
 m_reduced = (25.61, 25.62)
-p_ion = tg51.p_ion(voltage_reference=300, voltage_reduced=150, m_reference=m_reference, m_reduced=m_reduced)
+p_ion = tg51.p_ion(
+    voltage_reference=300,
+    voltage_reduced=150,
+    m_reference=m_reference,
+    m_reduced=m_reduced,
+)
 
 # Section 9 (M corrected)
-m_corr = tg51.m_corrected(p_ion=p_ion, p_tp=p_tp, p_elec=P_ELEC, p_pol=p_pol, m_reference=m_reference)
+m_corr = tg51.m_corrected(
+    p_ion=p_ion, p_tp=p_tp, p_elec=P_ELEC, p_pol=p_pol, m_reference=m_reference
+)
 
 # Section 10 (dose to water @ 10cm)
-dose_10 = m_corr*kq*ND_w
+dose_10 = m_corr * kq * ND_w
 dose_10_per_mu = dose_10 / MU
 
 # Section 11 (dose/MU to water @ dmax)

docs/source/code_snippets/trs398_class.py

@@ -1,32 +1,34 @@
 """A script to calculate TRS-398 dose using pylinac classes and following the TRS-398 photon form"""
 from pylinac.calibration import trs398
 
-
 ENERGY = 6
 TEMP = 22.1
 PRESS = trs398.mmHg2kPa(755.0)
-CHAMBER = '30013'  # PTW
+CHAMBER = "30013"  # PTW
 K_ELEC = 1.000
 ND_w = 5.443  # Gy/nC
 MU = 200
 CLINICAL_PDD = 66.5
 
 trs398_6x = trs398.TRS398Photon(
-    unit='TrueBeam1',
-    setup='SSD',
+    unit="TrueBeam1",
+    setup="SSD",
     chamber=CHAMBER,
-    temp=TEMP, press=PRESS,
+    temp=TEMP,
+    press=PRESS,
     n_dw=ND_w,
     clinical_pdd_zref=CLINICAL_PDD,
-    tpr2010=(38.2/66.6),
+    tpr2010=(38.2 / 66.6),
     energy=ENERGY,
     fff=False,
     k_elec=K_ELEC,
-    voltage_reference=-300, voltage_reduced=-150,
+    voltage_reference=-300,
+    voltage_reduced=-150,
     m_reference=(25.65, 25.66, 25.65),
     m_opposite=(25.64, 25.65, 25.65),
     m_reduced=(25.64, 25.63, 25.63),
-    mu=MU, tissue_correction=1.0
+    mu=MU,
+    tissue_correction=1.0,
 )
 
 # Done!
@@ -43,4 +45,8 @@
 print(trs398_6x.dose_mu_zmax_adjusted)
 
 # generate a PDF for record-keeping
-trs398_6x.publish_pdf('TB1 6MV TRS-398.pdf', notes=['My notes', 'I used Pylinac to do this; so easy!'], open_file=False)
+trs398_6x.publish_pdf(
+    "TB1 6MV TRS-398.pdf",
+    notes=["My notes", "I used Pylinac to do this; so easy!"],
+    open_file=False,
+)

docs/source/code_snippets/trs398_function.py

@@ -1,26 +1,38 @@
 """A script to calculate TRS-398 dose using pylinac functions and following the TRS-398 photon form"""
 from pylinac.calibration import trs398
 
-
 TEMP = 22.1
 PRESS = trs398.mmHg2kPa(755.0)
-CHAMBER = '30013'  # PTW
+CHAMBER = "30013"  # PTW
 K_ELEC = 1.000
 ND_w = 5.443  # Gy/nC
 MU = 200
 
 
 # Section 3 (dosimeter corrections)
 k_tp = trs398.k_tp(temp=TEMP, press=PRESS)
-k_pol = trs398.k_pol(m_reference=(25.66, 25.67, 25.66), m_opposite=(25.65, 25.66, 25.66))
-k_s = trs398.k_s(voltage_reference=300, voltage_reduced=150,
-                 m_reference=(25.66, 25.67, 25.66), m_reduced=(25.63, 25.65, 25.64))
-m_corrected = trs398.m_corrected(m_reference=(25.66, 25.67, 25.66),
-                                 k_tp=k_tp, k_elec=K_ELEC, k_pol=k_pol, k_s=k_s) \
-              / MU
+k_pol = trs398.k_pol(
+    m_reference=(25.66, 25.67, 25.66), m_opposite=(25.65, 25.66, 25.66)
+)
+k_s = trs398.k_s(
+    voltage_reference=300,
+    voltage_reduced=150,
+    m_reference=(25.66, 25.67, 25.66),
+    m_reduced=(25.63, 25.65, 25.64),
+)
+m_corrected = (
+    trs398.m_corrected(
+        m_reference=(25.66, 25.67, 25.66),
+        k_tp=k_tp,
+        k_elec=K_ELEC,
+        k_pol=k_pol,
+        k_s=k_s,
+    )
+    / MU
+)
 
 # Section 4 (kQ + dose at zref)
-kq = trs398.kq_photon(chamber=CHAMBER, tpr=(39.2/68.1))
+kq = trs398.kq_photon(chamber=CHAMBER, tpr=(39.2 / 68.1))
 dose_mu_zref = m_corrected * ND_w * kq
 
 # Section 5 (Dose at zmax)