merge devel to master (v0.12.1) (#1507)

Author: njzjz

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "devel"

.github/workflows/test.yml

@@ -21,7 +21,9 @@ jobs:
       run: pip install -e .[test]
     - name: Test
       run: coverage run --source=./dpgen -m unittest -v && coverage report
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   pass:
     needs: [build]
     runs-on: ubuntu-latest

.mailmap

@@ -0,0 +1 @@
+Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     # there are many log files in tests
     # TODO: seperate py files and log files
@@ -28,7 +28,7 @@ repos:
 
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.3
+    rev: v0.3.5
     hooks:
     - id: ruff
       args: ["--fix"]

MANIFEST.in

@@ -0,0 +1,4 @@
+prune conda
+prune doc
+prune tests
+prune examples

README.md

@@ -23,10 +23,10 @@ Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and
 
 ## Download and Install
 
-DP-GEN only supports Python 3.9 and above. You can use one of the following methods to install DP-GEN:
+DP-GEN only supports Python 3.9 and above. You can [setup a conda/pip environment](https://docs.deepmodeling.com/faq/conda.html), and then use one of the following methods to install DP-GEN:
 
 - Install via pip: `pip install dpgen`
-- Install via conda: `conda install -c conda-forge dpgen``
+- Install via conda: `conda install -c conda-forge dpgen`
 - Install from source code: `git clone https://github.com/deepmodeling/dpgen && pip install ./dpgen`
 
 To test if the installation is successful, you may execute

dpgen/auto_test/lib/lammps.py

@@ -189,9 +189,7 @@ def make_lammps_eval(conf, type_map, interaction, param):
     ret += (
         "thermo_style    custom step pe pxx pyy pzz pxy pxz pyz lx ly lz vol c_mype\n"
     )
-    ret += (
-        "dump            1 all custom 100 dump.relax id type xs ys zs fx fy fz\n"
-    )  # 06/09 give dump.relax
+    ret += "dump            1 all custom 100 dump.relax id type xs ys zs fx fy fz\n"  # 06/09 give dump.relax
     ret += "run    0\n"
     ret += "variable        N equal count(all)\n"
     ret += "variable        V equal vol\n"

dpgen/auto_test/lib/mfp_eosfit.py

@@ -1441,16 +1441,7 @@ def ext_velp(
     )
     for i in range(ndata):
         fw.write(
-            "{:12.6f}\t{:12.6f}\t{:12.6f}\t{:12.6f}\t{:12.6f}\t{:12.6f}\t{:12.6f}\t{:12.6f}\n".format(
-                vv[i],
-                ee[i],
-                cellaa[i],
-                cellbb[i],
-                cellcc[i],
-                cellbaba[i],
-                cellcaca[i],
-                cellca_cal[i],
-            )
+            f"{vv[i]:12.6f}\t{ee[i]:12.6f}\t{cellaa[i]:12.6f}\t{cellbb[i]:12.6f}\t{cellcc[i]:12.6f}\t{cellbaba[i]:12.6f}\t{cellcaca[i]:12.6f}\t{cellca_cal[i]:12.6f}\n"
         )
         fw.flush()
     fw.close()
@@ -1662,9 +1653,7 @@ def lsqfit_eos(
     )
     for i in range(len(vol)):
         fve.write(
-            "{:20f}\t{:20f}\t{:20f}\t{:20f}\n".format(
-                vol[i], repro_en[i], en[i], 100 * np.abs((en[i] - repro_en[i]) / en[i])
-            )
+            f"{vol[i]:20f}\t{repro_en[i]:20f}\t{en[i]:20f}\t{100 * np.abs((en[i] - repro_en[i]) / en[i]):20f}\n"
         )
         fve.flush()
         p_tmp = repro_press[i]

dpgen/auto_test/lib/pwscf.py

@@ -72,12 +72,7 @@ def _make_pwscf_03_config(sys_data):
     cc = 0
     for ii in range(ntypes):
         for jj in range(atom_numbs[ii]):
-            ret += "{} {:f} {:f} {:f}\n".format(
-                atom_names[ii],
-                coordinates[cc][0],
-                coordinates[cc][1],
-                coordinates[cc][2],
-            )
+            ret += f"{atom_names[ii]} {coordinates[cc][0]:f} {coordinates[cc][1]:f} {coordinates[cc][2]:f}\n"
             cc += 1
     return ret
 

dpgen/auto_test/reproduce.py

@@ -153,12 +153,7 @@ def post_repro(
             output_ener_tot.extend(output_task_result["energies"])
 
             init_epa = init_ener[jj - idid] / natoms
-            ptr_data += "{} {:7.3f}  {:7.3f}  {:7.3f}\n".format(
-                ii,
-                init_epa,
-                output_epa,
-                output_epa - init_epa,
-            )
+            ptr_data += f"{ii} {init_epa:7.3f}  {output_epa:7.3f}  {output_epa - init_epa:7.3f}\n"
         idid += nframe
         output_ener = np.array(output_ener)
         output_ener = np.reshape(output_ener, [-1, 1])