Merge branch 'master' into dp/nangrad-bdryerr-coils

.github/dependabot.yml

@@ -7,6 +7,36 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "weekly"
+    groups:
+      # group similar dependencies together into fewer PRs
+      docs:
+        patterns:
+          - "sphinx"
+      linting:
+        patterns:
+          - "flake8"
+          - "black"
+          - "pre-commit"
+      testing:
+        patterns:
+          - "pytest"
+          - "qic"
+          - "qsc"
+          - "shapely"
+      minor_packages:
+        patterns:
+          - "colorama"
+          - "nvgpu"
+          - "psutil"
+          - "pylatexenc"
+          - "termcolor"
+      jax:
+        patterns:
+          - "jax"
+          - "diffrax"
+          - "interpax"
+          - "orthax"
+          - "quadax"
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:

.github/workflows/update_notebook_examples.yml

@@ -0,0 +1,75 @@
+name: Update Notebooks and Examples
+on:
+  schedule:
+    # runs on the first of every month at noon
+    - cron: '00 12 1 * *'
+
+jobs:
+  create_issue:
+    name: Create issues to update notebooks and examples
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Create issue to update notebooks
+        run: |
+          if [[ $CLOSE_PREVIOUS == true ]]; then
+            previous_issue_number=$(gh issue list \
+              --label "$LABELS" \
+              --json number \
+              --jq '.[0].number')
+            if [[ -n $previous_issue_number ]]; then
+              gh issue close "$previous_issue_number"
+              gh issue unpin "$previous_issue_number"
+            fi
+          fi
+          new_issue_url=$(gh issue create \
+            --title "$TITLE" \
+            --assignee "$ASSIGNEES" \
+            --label "$LABELS" \
+            --body "$BODY")
+          if [[ $PINNED == true ]]; then
+            gh issue pin "$new_issue_url"
+          fi
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          TITLE: Update Notebooks
+          ASSIGNEES: f0uriest, dpanici, ddudt, rahulgaur104, kianorr, YigitElma
+          LABELS: monthly_update_notebooks
+          BODY: |
+            Reminder to check that notebooks evaluate correctly, and to update
+            if necessary.
+          PINNED: false
+          CLOSE_PREVIOUS: true
+      - name: Create issue to update notebooks
+        run: |
+            if [[ $CLOSE_PREVIOUS == true ]]; then
+                previous_issue_number=$(gh issue list \
+                --label "$LABELS" \
+                --json number \
+                --jq '.[0].number')
+                if [[ -n $previous_issue_number ]]; then
+                gh issue close "$previous_issue_number"
+                gh issue unpin "$previous_issue_number"
+                fi
+            fi
+            new_issue_url=$(gh issue create \
+                --title "$TITLE" \
+                --assignee "$ASSIGNEES" \
+                --label "$LABELS" \
+                --body "$BODY")
+            if [[ $PINNED == true ]]; then
+                gh issue pin "$new_issue_url"
+            fi
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          TITLE: Update Examples
+          ASSIGNEES: f0uriest, dpanici, ddudt, rahulgaur104, kianorr, YigitElma
+          LABELS: monthly_update_examples
+          BODY: |
+              Reminder to check that examples run correctly, and to update
+              if necessary.
+          PINNED: false
+          CLOSE_PREVIOUS: true

.pre-commit-config.yaml

@@ -1,11 +1,11 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 24.10.0
     hooks:
       - id: black-jupyter
         log_file: devtools/pre-commit.log
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
         log_file: devtools/pre-commit.log
@@ -22,20 +22,20 @@ repos:
       - id: no-commit-to-branch
         log_file: devtools/pre-commit.log
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)
         args: ["--profile", "black"]
         log_file: devtools/pre-commit.log
   - repo: https://github.com/PyCQA/flake8
-    rev: "5.0.4"
+    rev: "7.1.1"
     hooks:
       - id: flake8
         additional_dependencies: ["flake8-docstrings", "flake8-eradicate", "flake8-isort"]
         log_file: devtools/pre-commit.log
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.0
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
         log_file: devtools/pre-commit.log

desc/__main__.py

@@ -37,7 +37,7 @@ def main(cl_args=sys.argv[1:]):
         and (inputs[-1]["pres_ratio"] is None)
         and (inputs[-1]["bdry_ratio"] is None)
     ):
-        eq = Equilibrium(**inputs[-1], check_kwargs=False)
+        eq = Equilibrium(**inputs[-1], check_kwargs=False, ensure_nested=False)
         equil_fam = EquilibriaFamily.solve_continuation_automatic(
             eq,
             objective=inputs[-1]["objective"],

desc/equilibrium/utils.py

@@ -141,6 +141,7 @@ def parse_axis(axis, NFP=1, sym=True, surface=None):
             axis[:, 1],
             axis[:, 2],
             axis[:, 0].astype(int),
+            axis[:, 0].astype(int),
             NFP=NFP,
             sym=sym,
             name="axis",

desc/examples/ATF

@@ -34,10 +34,6 @@ l:   0	p =   5.00000000E+05	i =   -3.50000000E-01
 l:   2	p =  -1.00000000E+06	i =   -6.50000000E-01
 l:   4	p =   5.00000000E+05	i =   0.00000000E+00
 
-# magnetic axis initial guess
-n:   0	R0 =   2.10000000E+00	Z0 =   0.00000000E+00
-n:   1	R0 =   0.10000000E+00	Z0 =   0.10000000E+00
-
 # fixed-boundary surface shape
 m:  -2	n:  -1	R1 =  -2.50000000E-02	Z1 =   0.00000000E+00
 m:  -2	n:   0	R1 =   0.00000000E+00	Z1 =  -6.75000000E-03

desc/examples/HELIOTRON

@@ -14,15 +14,15 @@ M_grid = 12, 18
 N_grid =  0,  0,  6
 
 # continuation parameters
-bdry_ratio = 0, 0, 1
+bdry_ratio = 0, 0, 0.5, 1
 pres_ratio = 0, 1, 1
 pert_order = 2
 
 # solver tolerances
 ftol = 1e-2
 xtol = 1e-6
 gtol = 1e-6
-maxiter = 100
+maxiter = 50
 
 # solver methods
 optimizer         = lsq-exact

desc/examples/NCSX

@@ -20,7 +20,7 @@ pert_order = 2.0
 # solver tolerances
 ftol = 1e-2
 xtol = 1e-6
-gtol = 1e-2
+gtol = 1e-8
 maxiter = 50
 
 # solver methods

desc/examples/W7-X

@@ -6,25 +6,19 @@ NFP =  5
 Psi = -2.13300000E+00
 
 # spectral resolution
-L_rad = 12,16,24
+L_rad  = 12
 M_pol  = 12
-N_tor  =   12
-M_grid =  16
-N_grid =   16
+N_tor  = 12
+M_grid = 16
+N_grid = 16
 
 # continuation parameters
-# because we specify these and a sequence for L_rad, it will not use the automatic continuation
-bdry_ratio=1.0
 pert_order = 2
 
 
 # solver methods
 optimizer         = lsq-exact
 objective         = force
-spectral_indexing = fringe
-ftol=1e-4
-xtol= 1e-6
-maxiter=150
 
 # pressure and rotational transform profiles
 l:   0	p =   1.85596929e+05	i =  -8.56047021e-01

desc/examples/regenerate_all_equilibria.py

@@ -4,43 +4,67 @@
 
 python3 regenerate_all_equilibria.py
 
-Copy the two lines below to the main code to run it on a GPU
-from desc import set_device
-set_device("gpu")
 """
+import argparse
 import glob
 import os
 import subprocess as spr
+import sys
+from pathlib import Path
 
-from desc.__main__ import main
-from desc.io import load
-from desc.vmec import VMECIO
+parser = argparse.ArgumentParser(
+    prog="regenerate_all_equilibria",
+)
+parser.add_argument(
+    "-o",
+    "--output",
+    metavar="output_dir",
+    help="Path to output files. If not specified, defaults to input dir",
+)
+parser.add_argument(
+    "--gpu",
+    "-g",
+    action="store_true",
+    help="Use GPU if available. If more than one are available, selects the "
+    + "GPU with most available memory. ",
+)
+parser.add_argument(
+    "--noprecise",
+    action="store_true",
+    help="Don't regenerate precise QS equilibria.",
+)
+
+
+args = parser.parse_args(sys.argv[1:])
 
 pwd = os.getcwd()
+if args.output:
+    output_path = os.path.abspath(args.output)
+else:
+    output_path = pwd
+
+Path(output_path).mkdir(parents=True, exist_ok=True)
+
+files = sorted(glob.glob(pwd + "/*.h5"))
+print("Regenerating files:")
+for f in files:
+    print(f)
+print("saving to: ", output_path)
+names = [f.split("/")[-1].split(".")[0].replace("_output", "") for f in files]
+names = [f for f in names if "precise" not in f]
+
+for fname in names:
+    print(f"Running the input file {fname} \n")
+    cargs = [
+        "desc",
+        fname,
+        "-vv",
+        f"-o {os.path.join(output_path, fname + '_output.h5')}",
+    ]
+    if args.gpu:
+        cargs += ["-g"]
+    spr.run(cargs)
 
-for fname in glob.glob(pwd + "/*.h5"):
-    if (
-        fname.split(".")[-1] == "h5"
-        and os.path.isfile(fname.split(".")[-1] + ".nc") is True
-        and fname.split(".")[0].split("/")[-1].split("_")[0] != "precise"
-    ):
-        finputname = fname.split(".")[0].split("/")[-1].split("_")[0]
-        print(f"Running the input file {finputname} \n")
-        main(cl_args=[str(f"{finputname}"), "-vv"])
-        # save wout file
-        eq = load(f"{pwd}/{finputname}")[-1]
-        VMECIO.save(eq, "wout_" + fname + ".nc", surfs=256)
-    elif (
-        fname.split(".")[-1] == "h5"
-        and os.path.isfile(fname + ".nc") is False
-        and fname.split(".")[0].split("/")[-1].split("_")[0] != "precise"
-    ):
-        finputname = fname.split(".")[0].split("/")[-1].split("_")[0]
-        print(f"Running the input file {finputname} \n")
-        main(cl_args=[str(f"{finputname}"), "-vv"])
-    else:
-        continue
-
-main(cl_args=["DSHAPE_CURRENT", "-vv"])
-spr.call(["python3 -u precise_QA.py"], shell=True)
-spr.call(["python3 -u precise_QH.py"], shell=True)
+if not args.noprecise:
+    spr.run(["python3", "-u", "precise_QA.py"])
+    spr.run(["python3", "-u", "precise_QH.py"])