Merge pull request #6 from PrincetonUniversity/lint_deploy

PrincetonUniversity · Sep 18, 2024 · 6e5273c · 6e5273c
2 parents 9e57031 + 44271fa
commit 6e5273c
Show file tree

Hide file tree

Showing 14 changed files with 903 additions and 583 deletions.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -6,5 +6,5 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: chartboost/ruff-action@v1
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.3
+  rev: v0.6.5
   hooks:
   - id: ruff
     types_or: [python, pyi, jupyter]

diff --git a/.ruff.toml b/.ruff.toml
@@ -0,0 +1,2 @@
+[lint]
+ignore = ["E741"]
diff --git a/astro_tigress/athena_read.py b/astro_tigress/athena_read.py
diff --git a/astro_tigress/map_circular_beam.py b/astro_tigress/map_circular_beam.py
@@ -2,57 +2,60 @@
 import math
 from scipy.integrate import quad
 
+
 def get_gauss_stamp(n):
     nx = n
     ny = n
-    nxc = nx/2
-    nyc = ny/2
+    nxc = nx / 2
+    nyc = ny / 2
     ix = np.zeros((nx, ny))
     iy = np.zeros((nx, ny))
     for i in range(nx):
         for j in range(ny):
-            ix[i, j] = j-nyc
-            iy[i, j] = i-nxc
+            ix[i, j] = j - nyc
+            iy[i, j] = i - nxc
+
     def gauss(x):
         sigmax = 0.5
-        ret = 1./(np.sqrt(2*math.pi)*sigmax) * np.exp(-0.5*(x/sigmax)**2) 
+        ret = 1.0 / (np.sqrt(2 * math.pi) * sigmax) * np.exp(-0.5 * (x / sigmax) ** 2)
         return ret
+
     stamp = np.zeros((nx, ny))
     for i in range(nx):
         for j in range(ny):
             x1 = ix[i, j] - 0.5
-            x2 = x1 + 1.
+            x2 = x1 + 1.0
             y1 = iy[i, j] - 0.5
-            y2 = y1 + 1.
+            y2 = y1 + 1.0
             inte = quad(gauss, x1, x2)[0] * quad(gauss, y1, y2)[0]
             stamp[i, j] = inte
     return stamp
 
-#average data using a stamp
+
+# average data using a stamp
 def stamp_avg(data, stamp):
     nxd, nyd = data.shape
     nxs, nys = stamp.shape
     ret = np.zeros(data.shape)
-    nxc = nxs/2
-    nyc = nys/2
+    nxc = nxs / 2
+    nyc = nys / 2
     ix = np.zeros((nxs, nys))
     iy = np.zeros((nxs, nys))
     for i in range(nxs):
         for j in range(nys):
-            ix[i, j] = i-nxc
-            iy[i, j] = j-nyc
+            ix[i, j] = i - nxc
+            iy[i, j] = j - nyc
     for i in range(nxd):
         for j in range(nyd):
             for istamp in range(nxs):
                 for jstamp in range(nys):
                     iret = i + ix[istamp, jstamp]
                     jret = j + iy[istamp, jstamp]
-                    if (iret >= 0) and (iret < nxd
-                        ) and (jret >= 0) and (jret < nyd):
-                        ret[iret, jret] += data[i, j]*stamp[istamp, jstamp]
+                    if (iret >= 0) and (iret < nxd) and (jret >= 0) and (jret < nyd):
+                        ret[iret, jret] += data[i, j] * stamp[istamp, jstamp]
     return ret
 
+
 def map_circular_beam(data, nstamp=9):
     stamp = get_gauss_stamp(nstamp)
     return stamp_avg(data, stamp)
-
diff --git a/astro_tigress/tigress_read.py b/astro_tigress/tigress_read.py
@@ -168,9 +168,7 @@ def _download_file(self, f):
 
         target = osp.join(self.dir_master, f)
         if osp.isfile(target):
-            print(
-                "{} ({:.5f}GB) already exists".format(f, osp.getsize(target) / 2**30)
-            )
+            print("{} ({:.5f}GB) already exists".format(f, osp.getsize(target) / 2**30))
             while True:
                 answer = input("overwrite? [y/n]:")
                 if answer.lower() in ["y", "n"]:
@@ -184,7 +182,7 @@ def _download_file(self, f):
         req = urllib.request.Request(source)
 
         try:
-            response = urllib.request.urlopen(req)
+            urllib.request.urlopen(req)
         except URLError as e:
             if hasattr(e, "reason"):
                 print("We failed to reach a server.")

diff --git a/astro_tigress/tigress_utils.py b/astro_tigress/tigress_utils.py
@@ -1,27 +1,28 @@
 import os
 import shutil
 
+
 def copy_file(fn_old, fn_new):
     """Copy file from old to new location. Make new directory if needed.
     Raise warning if old file does not exist.
     inputs:
         fn_old: string, old filename
         fn_new: string, new filename"""
     if fn_old == fn_new:
-        raise ValueError('New filename cannot be the same as the original one.')
+        raise ValueError("New filename cannot be the same as the original one.")
     if os.path.isfile(fn_old):
         if os.path.isfile(fn_new):
-            print("New file already exists: "+fn_new)
+            print("New file already exists: " + fn_new)
             while True:
                 answer = input("Overwrite? (y/n):")
                 if answer == "y":
                     break
                 elif answer == "n":
-                    return          
+                    return
         dir_new = os.path.dirname(fn_new)
         if not os.path.exists(dir_new):
             os.makedirs(dir_new)
         shutil.copyfile(fn_old, fn_new)
     else:
-        raise RuntimeError("file does not exist: "+fn_old)
+        raise RuntimeError("file does not exist: " + fn_old)
     return
diff --git a/astro_tigress/ytathena.py b/astro_tigress/ytathena.py
@@ -39,7 +39,7 @@ def __init__(self, fname=os.path.join(dirpath, "coolftn.txt")):
         self.nT = len(self.T1)
 
     def get_Tidx(self, T):
-        if type(T) == np.ndarray:
+        if type(T) is np.ndarray:
             Tidx = np.log10(T / self.Tmin) / self.dT
             Tidx[np.where(T < self.Tmin)] = 0
             Tidx[np.where(T >= self.Tmax)] = self.nT - 2

diff --git a/docs/example_2-synthetic-dustpol.ipynb b/docs/example_2-synthetic-dustpol.ipynb
@@ -35,14 +35,16 @@
     "# add path to astro_tigress module\n",
     "# this can also be done using PYTHONPATH environment variable\n",
     "import sys\n",
-    "sys.path.insert(0,'../')\n",
+    "\n",
+    "sys.path.insert(0, \"../\")\n",
     "\n",
     "import astro_tigress\n",
+    "\n",
     "# Need to set the master directory where the data is stored\n",
     "dir_master = \"../data/\"\n",
     "# name of the simulation model\n",
-    "model_id = \"R8_4pc\" \n",
-    "model = astro_tigress.Model(model_id,dir_master) #reading the model information"
+    "model_id = \"R8_4pc\"\n",
+    "model = astro_tigress.Model(model_id, dir_master)  # reading the model information"
    ]
   },
   {
@@ -51,7 +53,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#load the MHD data set for the snapshot ivtk=300\n",
+    "# load the MHD data set for the snapshot ivtk=300\n",
     "model.load(300, dataset=\"MHD\")"
    ]
   },
@@ -69,11 +71,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Temp = model.MHD.grid[('gas','temperature')].in_units(\"K\").value.T\n",
-    "nH = model.MHD.grid[('gas','nH')].in_units(\"cm**-3\").value.T\n",
-    "Bx = model.MHD.grid[('gas','magnetic_field_x')].in_units(\"uG\").value.T\n",
-    "By = model.MHD.grid[('gas','magnetic_field_y')].in_units(\"uG\").value.T\n",
-    "Bz = model.MHD.grid[('gas','magnetic_field_z')].in_units(\"uG\").value.T"
+    "Temp = model.MHD.grid[(\"gas\", \"temperature\")].in_units(\"K\").value.T\n",
+    "nH = model.MHD.grid[(\"gas\", \"nH\")].in_units(\"cm**-3\").value.T\n",
+    "Bx = model.MHD.grid[(\"gas\", \"magnetic_field_x\")].in_units(\"uG\").value.T\n",
+    "By = model.MHD.grid[(\"gas\", \"magnetic_field_y\")].in_units(\"uG\").value.T\n",
+    "Bz = model.MHD.grid[(\"gas\", \"magnetic_field_z\")].in_units(\"uG\").value.T"
    ]
   },
   {
@@ -90,9 +92,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "xcc = model.MHD.grid[(\"gas\",\"x\")][:,0,0].to('pc').value\n",
-    "ycc = model.MHD.grid[(\"gas\",\"y\")][0,:,0].to('pc').value\n",
-    "zcc = model.MHD.grid[(\"gas\",\"z\")][0,0,:].to('pc').value"
+    "xcc = model.MHD.grid[(\"gas\", \"x\")][:, 0, 0].to(\"pc\").value\n",
+    "ycc = model.MHD.grid[(\"gas\", \"y\")][0, :, 0].to(\"pc\").value\n",
+    "zcc = model.MHD.grid[(\"gas\", \"z\")][0, 0, :].to(\"pc\").value"
    ]
   },
   {
@@ -109,8 +111,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dx_pc = model.MHD.grid[(\"gas\",\"dx\")][0,0,0].to('pc').value\n",
-    "dx_cm = model.MHD.grid[(\"gas\",\"dx\")][0,0,0].to('cm').value"
+    "dx_pc = model.MHD.grid[(\"gas\", \"dx\")][0, 0, 0].to(\"pc\").value\n",
+    "dx_cm = model.MHD.grid[(\"gas\", \"dx\")][0, 0, 0].to(\"cm\").value"
    ]
   },
   {
@@ -128,7 +130,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "I,Q,U = calc_IQU(nH,Bx,By,Bz,dx_pc,los='y')"
+    "I, Q, U = calc_IQU(nH, Bx, By, Bz, dx_pc, los=\"y\")"
    ]
   },
   {
@@ -156,24 +158,24 @@
     }
    ],
    "source": [
-    "fig, axes = plt.subplots(1,2, figsize=(12,5))\n",
+    "fig, axes = plt.subplots(1, 2, figsize=(12, 5))\n",
     "# integration along the y-axis (edge on view)\n",
     "plt.sca(axes[0])\n",
-    "NH = nH.sum(axis=1)*dx_cm\n",
+    "NH = nH.sum(axis=1) * dx_cm\n",
     "\n",
-    "plt.pcolormesh(xcc,zcc,NH,vmax=1.e22,shading='nearest')\n",
-    "plt.gca().set_aspect('equal')\n",
-    "plt.xlabel('x[pc]')\n",
-    "plt.ylabel('z[pc]')\n",
-    "cbar = plt.colorbar(label=r'$N_H\\,[{\\rm cm^{-2}}]$')\n",
+    "plt.pcolormesh(xcc, zcc, NH, vmax=1.0e22, shading=\"nearest\")\n",
+    "plt.gca().set_aspect(\"equal\")\n",
+    "plt.xlabel(\"x[pc]\")\n",
+    "plt.ylabel(\"z[pc]\")\n",
+    "cbar = plt.colorbar(label=r\"$N_H\\,[{\\rm cm^{-2}}]$\")\n",
     "\n",
     "plt.sca(axes[1])\n",
     "\n",
-    "plt.pcolormesh(xcc,zcc,I,vmax=5,shading='nearest')\n",
-    "plt.gca().set_aspect('equal')\n",
-    "plt.xlabel('x[pc]')\n",
-    "plt.ylabel('z[pc]')\n",
-    "cbar = plt.colorbar(label=r'$I$')"
+    "plt.pcolormesh(xcc, zcc, I, vmax=5, shading=\"nearest\")\n",
+    "plt.gca().set_aspect(\"equal\")\n",
+    "plt.xlabel(\"x[pc]\")\n",
+    "plt.ylabel(\"z[pc]\")\n",
+    "cbar = plt.colorbar(label=r\"$I$\")"
    ]
   },
   {
@@ -190,7 +192,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "P = np.sqrt(Q**2+U**2)"
+    "P = np.sqrt(Q**2 + U**2)"
    ]
   },
   {
@@ -210,34 +212,34 @@
     }
    ],
    "source": [
-    "fig, axes = plt.subplots(2,2, figsize=(13,10))\n",
+    "fig, axes = plt.subplots(2, 2, figsize=(13, 10))\n",
     "axes = axes.flatten()\n",
     "# integration along the y-axis (edge on view)\n",
     "plt.sca(axes[0])\n",
-    "plt.pcolormesh(xcc,zcc,I,vmax=5,shading='nearest')\n",
-    "plt.gca().set_aspect('equal')\n",
-    "plt.xlabel('x[pc]')\n",
-    "plt.ylabel('z[pc]')\n",
-    "cbar = plt.colorbar(label=r'$I$')\n",
+    "plt.pcolormesh(xcc, zcc, I, vmax=5, shading=\"nearest\")\n",
+    "plt.gca().set_aspect(\"equal\")\n",
+    "plt.xlabel(\"x[pc]\")\n",
+    "plt.ylabel(\"z[pc]\")\n",
+    "cbar = plt.colorbar(label=r\"$I$\")\n",
     "plt.sca(axes[1])\n",
-    "plt.pcolormesh(xcc,zcc,P/I,vmax=0.2,shading='nearest')\n",
-    "plt.gca().set_aspect('equal')\n",
-    "plt.xlabel('x[pc]')\n",
-    "plt.ylabel('z[pc]')\n",
-    "cbar = plt.colorbar(label=r'$P/I$')\n",
+    "plt.pcolormesh(xcc, zcc, P / I, vmax=0.2, shading=\"nearest\")\n",
+    "plt.gca().set_aspect(\"equal\")\n",
+    "plt.xlabel(\"x[pc]\")\n",
+    "plt.ylabel(\"z[pc]\")\n",
+    "cbar = plt.colorbar(label=r\"$P/I$\")\n",
     "\n",
     "plt.sca(axes[2])\n",
-    "plt.pcolormesh(xcc,zcc,Q,vmin=-0.1,vmax=0.1,shading='nearest',cmap=plt.cm.RdBu)\n",
-    "plt.gca().set_aspect('equal')\n",
-    "plt.xlabel('x[pc]')\n",
-    "plt.ylabel('z[pc]')\n",
-    "cbar = plt.colorbar(label=r'$Q$')\n",
+    "plt.pcolormesh(xcc, zcc, Q, vmin=-0.1, vmax=0.1, shading=\"nearest\", cmap=plt.cm.RdBu)\n",
+    "plt.gca().set_aspect(\"equal\")\n",
+    "plt.xlabel(\"x[pc]\")\n",
+    "plt.ylabel(\"z[pc]\")\n",
+    "cbar = plt.colorbar(label=r\"$Q$\")\n",
     "plt.sca(axes[3])\n",
-    "plt.pcolormesh(xcc,zcc,U,vmin=-0.1,vmax=0.1,shading='nearest',cmap=plt.cm.RdBu)\n",
-    "plt.gca().set_aspect('equal')\n",
-    "plt.xlabel('x[pc]')\n",
-    "plt.ylabel('z[pc]')\n",
-    "cbar = plt.colorbar(label=r'$U$')"
+    "plt.pcolormesh(xcc, zcc, U, vmin=-0.1, vmax=0.1, shading=\"nearest\", cmap=plt.cm.RdBu)\n",
+    "plt.gca().set_aspect(\"equal\")\n",
+    "plt.xlabel(\"x[pc]\")\n",
+    "plt.ylabel(\"z[pc]\")\n",
+    "cbar = plt.colorbar(label=r\"$U$\")"
    ]
   },
   {