refactor: cat is fluid

.github/workflows/ci.yml

@@ -6,14 +6,14 @@ on:
       - 'master'
       - 'dev'
     paths:
-      - catalyner/**
+      - catflow/**
       - tests/**
       - .github/workflows/ci.yml
       - pyproject.toml
       - poetry.lock
   pull_request:
     paths:
-      - catalyner/**
+      - catflow/**
       - tests/**
       - .github/workflows/ci.yml
       - pyproject.toml
@@ -52,6 +52,6 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          poetry run coverage run --source=./catalyner -m pytest -v tests/
+          poetry run coverage run --source=./catflow -m pytest -v tests/
           poetry run coverage report
           poetry run coveralls --service=github

.github/workflows/deploy_docs.yml

@@ -7,7 +7,7 @@ on:
       - docs/**
       - README.md
       - mkdocs.yml
-      - catalyner/**
+      - catflow/**
       - .github/workflows/deploy_docs.yml
 jobs:
   deploy:

README.md

@@ -1,12 +1,12 @@
 # Catlyner
 
-[![Python package](https://github.com/Cloudac7/catalyner/actions/workflows/ci.yml/badge.svg)](https://github.com/Cloudac7/catalyner/actions/workflows/ci.yml)
-[![Coverage Status](https://coveralls.io/repos/github/Cloudac7/catalyner/badge.svg?branch=master)](https://coveralls.io/github/Cloudac7/catalyner?branch=master)
+[![Python package](https://github.com/Cloudac7/catflow/actions/workflows/ci.yml/badge.svg)](https://github.com/Cloudac7/catflow/actions/workflows/ci.yml)
+[![Coverage Status](https://coveralls.io/repos/github/Cloudac7/catflow/badge.svg?branch=master)](https://coveralls.io/github/Cloudac7/catflow?branch=master)
 
 
 Machine learning aided catalysis reaction free energy calculation and post-analysis workflow, thus, analyzer for catalysis.
 
-Mainly developed on MacOS Catalina.
+As is known to all, cat is fluid and thus cat flows. 🐱
 
 > Former Miko-Analyzer
 
@@ -15,13 +15,13 @@ Mainly developed on MacOS Catalina.
 To install, clone the repository:
 
 ```
-git clone https://github.com/cloudac7/catalyner.git
+git clone https://github.com/cloudac7/catflow.git
 ```
 
 and then install with `pip`:
 
 ```
-cd catalyner
+cd catflow
 pip install .
 ```
 

catalyner/__main__.py → catflow/__main__.py

@@ -1,5 +1,5 @@
 import sys
 
 if __name__ == '__main__':
-    from catalyner.cmdline.base import cli
+    from catflow.cmdline.base import cli
     sys.exit(cli())

catalyner/cmdline/base.py → catflow/cmdline/base.py

@@ -3,7 +3,7 @@
 from importlib.metadata import entry_points
 
 
-entries = entry_points().get('catalyner.cmdline', [])
+entries = entry_points().get('catflow.cmdline', [])
 if entries != []:
     entries_cli = [i.load() for i in entries]
 else:

catalyner/metad/fes.py → catflow/metad/fes.py

@@ -9,9 +9,9 @@
 from numpy.typing import ArrayLike
 from matplotlib.colors import Colormap
 
-from catalyner.metad.hills import Hills
-from catalyner.graph.plotting import canvas_style
-from catalyner.utils.log_factory import logger
+from catflow.metad.hills import Hills
+from catflow.graph.plotting import canvas_style
+from catflow.utils.log_factory import logger
 
 
 class FreeEnergySurface:
@@ -20,7 +20,7 @@ class FreeEnergySurface:
 
     Usage:
     ```python
-    from catalyner.metad.fes import FreeEnergySurface
+    from catflow.metad.fes import FreeEnergySurface
     fes = FreeEnergySurface(hills)
     ```
 

catalyner/metad/profile.py → catflow/metad/profile.py

@@ -5,9 +5,9 @@
 from typing import List, Optional, Union
 from matplotlib.colors import Colormap
 
-from catalyner.graph.plotting import canvas_style
-from catalyner.metad.fes import FreeEnergySurface
-from catalyner.metad.hills import Hills
+from catflow.graph.plotting import canvas_style
+from catflow.metad.fes import FreeEnergySurface
+from catflow.metad.hills import Hills
 
 
 class FreeEnergyProfile:

catalyner/metad/string.py → catflow/metad/string.py

@@ -15,8 +15,8 @@
 from scipy.interpolate import Rbf, griddata, interp1d, RegularGridInterpolator
 from typing import Literal, List, Union, Tuple, Optional
 
-from catalyner.utils import logger
-from catalyner.metad.fes import FreeEnergySurface
+from catflow.utils import logger
+from catflow.metad.fes import FreeEnergySurface
 
 
 class StringMethod:

catalyner/structure/cluster.py → catflow/structure/cluster.py

@@ -8,7 +8,7 @@
 from MDAnalysis import Universe
 
 
-from catalyner.structure.lindemann_index import LindemannIndex
+from catflow.structure.lindemann_index import LindemannIndex
 
 
 class Cluster(object):

catalyner/structure/dynamic_selection.py → catflow/structure/dynamic_selection.py

@@ -108,7 +108,7 @@ class AxisMaxDistance(AnalysisBase):
 
     Examples:
         >>> import MDAnalysis as mda
-        >>> from catalyner.structure.dynamic_selection import AxisMaxDistance
+        >>> from catflow.structure.dynamic_selection import AxisMaxDistance
         >>> u = mda.Universe("system.gro", "system.trr")
         >>> ag1 = u.select_atoms("protein")
         >>> ag2 = u.select_atoms("resname LIG")

catalyner/tesla/ai2_kit/exploration.py → catflow/tesla/ai2_kit/exploration.py

@@ -4,10 +4,10 @@
 
 import numpy as np
 
-from catalyner.utils.log_factory import logger
-from catalyner.utils.lammps import lammps_variable_parser
-from catalyner.tesla.base.exploration import ExplorationAnalyzer
-from catalyner.tesla.ai2_kit.task import CllAnalyzer
+from catflow.utils.log_factory import logger
+from catflow.utils.lammps import lammps_variable_parser
+from catflow.tesla.base.exploration import ExplorationAnalyzer
+from catflow.tesla.ai2_kit.task import CllAnalyzer
 
 
 def read_model_deviation(model_devi_path: Path):

catalyner/tesla/ai2_kit/labeling.py → catflow/tesla/ai2_kit/labeling.py

@@ -1,8 +1,8 @@
 import re
 
-from catalyner.tesla.base.labeling import LabelingAnalyzer
-from catalyner.tesla.ai2_kit.task import CllAnalyzer
-from catalyner.graph.plotting import canvas_style
+from catflow.tesla.base.labeling import LabelingAnalyzer
+from catflow.tesla.ai2_kit.task import CllAnalyzer
+from catflow.graph.plotting import canvas_style
 
 
 class CllLabelingAnalyzer(LabelingAnalyzer, CllAnalyzer):

catalyner/tesla/ai2_kit/task.py → catflow/tesla/ai2_kit/task.py

@@ -8,7 +8,7 @@
 from ai2_kit.core.checkpoint import set_checkpoint_file
 from ai2_kit.workflow.cll_mlp import CllWorkflowConfig
 
-from catalyner.tesla.base.task import BaseTask, BaseAnalyzer
+from catflow.tesla.base.task import BaseTask, BaseAnalyzer
 
 
 class CllTask(BaseTask):

catalyner/tesla/ai2_kit/training.py → catflow/tesla/ai2_kit/training.py

@@ -3,10 +3,10 @@
 import numpy as np
 from matplotlib import pyplot as plt
 
-from catalyner.utils import logger
-from catalyner.graph.plotting import canvas_style
-from catalyner.tesla.base.training import TrainingAnalyzer
-from catalyner.tesla.ai2_kit.task import CllAnalyzer, CllTask
+from catflow.utils import logger
+from catflow.graph.plotting import canvas_style
+from catflow.tesla.base.training import TrainingAnalyzer
+from catflow.tesla.ai2_kit.task import CllAnalyzer, CllTask
 
 
 class CllTrainingAnalyzer(TrainingAnalyzer, CllAnalyzer):

catalyner/tesla/base/exploration.py → catflow/tesla/base/exploration.py

@@ -11,9 +11,9 @@
 import seaborn as sns
 from matplotlib import pyplot as plt
 
-from catalyner.utils.log_factory import logger
-from catalyner.graph.plotting import canvas_style, square_grid
-from catalyner.tesla.base.task import BaseAnalyzer
+from catflow.utils.log_factory import logger
+from catflow.graph.plotting import canvas_style, square_grid
+from catflow.tesla.base.task import BaseAnalyzer
 
 
 def read_model_deviation(model_devi_path: Path):
@@ -251,7 +251,7 @@ def plot_single_iteration(
             kwargs (_type_, optional): Additional keyword arguments. Include other params, such as:
                 `temps`: please use the value of `group_by`, whose default input is `"temps"`.
                 `label_unit`: the unit of `select_value`, such as 'Å'.
-                Parameters of `canvas_style`: please refer to `catalyner.graph.plotting.canvas_style`.
+                Parameters of `canvas_style`: please refer to `catflow.graph.plotting.canvas_style`.
 
         Returns:
             Figure: A plot for different desired values.

catalyner/tesla/base/labeling.py → catflow/tesla/base/labeling.py

@@ -7,10 +7,10 @@
 from ase.io import read
 from matplotlib import pyplot as plt
 
-from catalyner.utils.log_factory import logger
-from catalyner.utils.log_factory import LogFactory
-from catalyner.tesla.base.task import BaseTask, BaseAnalyzer
-from catalyner.graph.plotting import canvas_style
+from catflow.utils.log_factory import logger
+from catflow.utils.log_factory import LogFactory
+from catflow.tesla.base.task import BaseTask, BaseAnalyzer
+from catflow.graph.plotting import canvas_style
 
 
 

catalyner/tesla/base/training.py → catflow/tesla/base/training.py

@@ -3,9 +3,9 @@
 import numpy as np
 from matplotlib import pyplot as plt
 
-from catalyner.utils import logger
-from catalyner.graph.plotting import canvas_style
-from catalyner.tesla.base.task import BaseAnalyzer, BaseTask
+from catflow.utils import logger
+from catflow.graph.plotting import canvas_style
+from catflow.tesla.base.task import BaseAnalyzer, BaseTask
 
 
 class TrainingAnalyzer(BaseAnalyzer):

catalyner/tesla/dpgen/exploration.py → catflow/tesla/dpgen/exploration.py

@@ -8,10 +8,10 @@
 import numpy as np
 from matplotlib import pyplot as plt
 
-from catalyner.utils.log_factory import logger
-from catalyner.graph.plotting import canvas_style, square_grid
-from catalyner.tesla.base.exploration import ExplorationAnalyzer, PlottingExploartion
-from catalyner.tesla.dpgen.task import DPAnalyzer
+from catflow.utils.log_factory import logger
+from catflow.graph.plotting import canvas_style, square_grid
+from catflow.tesla.base.exploration import ExplorationAnalyzer, PlottingExploartion
+from catflow.tesla.dpgen.task import DPAnalyzer
 
 
 class DPExplorationAnalyzer(ExplorationAnalyzer, DPAnalyzer):
@@ -95,7 +95,7 @@ def plot_single_iteration(
             kwargs (_type_, optional): Additional keyword arguments. Include other params, such as:
                 `temps`: please use the value of `group_by`, whose default input is `"temps"`.
                 `label_unit`: the unit of `select_value`, such as 'Å'.
-                Parameters of `canvas_style`: please refer to `catalyner.graph.plotting.canvas_style`.
+                Parameters of `canvas_style`: please refer to `catflow.graph.plotting.canvas_style`.
 
         Returns:
             Figure: A plot for different desired values.

catalyner/tesla/dpgen/labeling.py → catflow/tesla/dpgen/labeling.py

@@ -1,7 +1,7 @@
 from typing import Optional
 
-from catalyner.tesla.base.labeling import LabelingAnalyzer
-from catalyner.tesla.dpgen.task import DPTask, DPAnalyzer
+from catflow.tesla.base.labeling import LabelingAnalyzer
+from catflow.tesla.dpgen.task import DPTask, DPAnalyzer
 
 
 class DPLabelingAnalyzer(LabelingAnalyzer, DPAnalyzer):

catalyner/tesla/dpgen/task.py → catflow/tesla/dpgen/task.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 from typing import Optional
 
-from catalyner.tesla.base.task import BaseTask, BaseAnalyzer
+from catflow.tesla.base.task import BaseTask, BaseAnalyzer
 
 
 class DPTask(BaseTask):

catalyner/tesla/dpgen/training.py → catflow/tesla/dpgen/training.py

@@ -4,10 +4,10 @@
 import numpy as np
 from matplotlib import pyplot as plt
 
-from catalyner.utils import logger
-from catalyner.graph.plotting import canvas_style
-from catalyner.tesla.base.training import TrainingAnalyzer
-from catalyner.tesla.dpgen.task import DPAnalyzer
+from catflow.utils import logger
+from catflow.graph.plotting import canvas_style
+from catflow.tesla.base.training import TrainingAnalyzer
+from catflow.tesla.dpgen.task import DPAnalyzer
 
 class DPTrainingAnalyzer(TrainingAnalyzer, DPAnalyzer):
     """Analyzer for training tasks.

catalyner/utils/log_factory.py → catflow/utils/log_factory.py

@@ -6,7 +6,7 @@ class LogFactory(object):
     """
     For logging
     """
-    def __init__(self, logger=None, log_dir=None, log_name="catalyner.log"):
+    def __init__(self, logger=None, log_dir=None, log_name="catflow.log"):
         self.log_path = Path.cwd() if log_dir is None else Path(log_dir)
         self.logger = logging.getLogger(logger)
         self.logger.setLevel(logging.DEBUG)

docs/Usage/cluster_structures.md

@@ -6,7 +6,7 @@
 其他的参数请以可选参数形式传入。
 
 ```python
-from catalyner.structure.cluster import Cluster
+from catflow.structure.cluster import Cluster
 
 trajfile = "./dump.lammpstrj"
 c = Cluster(trajfile, topology_format="LAMMPSDUMP", dt=0.0005)

docs/Usage/dpgen_analysis.md

@@ -5,7 +5,7 @@
 首先，导入环境：
 
 ```python
-from catalyner.tesla.dpgen import DPTask
+from catflow.tesla.dpgen import DPTask
 ```
 
 加载DP-GEN工作目录：
@@ -26,7 +26,7 @@ t = DPTask(
 导入分析器（`DPAnalyzer`），这里我们选择训练，即：
 
 ```python
-from catalyner.tesla.dpgen.training import DPTrainingAnalyzer
+from catflow.tesla.dpgen.training import DPTrainingAnalyzer
 ```
 
 从任务初始化分析器实例：
@@ -51,7 +51,7 @@ fig.set_size_inches((12,12))
 类似地，我们也可以对模型的model deviation分布进行分析：
 
 ```python
-from catalyner.tesla.dpgen.exploration import DPExplorationAnalyzer
+from catflow.tesla.dpgen.exploration import DPExplorationAnalyzer
 ana = DPExplorationAnalyzer(t)
 ```
 

docs/Usage/metadyn.ipynb

@@ -50,7 +50,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from catalyner.metad.hills import Hills"
+    "from catflow.metad.hills import Hills"
    ]
   },
   {
@@ -93,7 +93,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from catalyner.metad.fes import FreeEnergySurface\n",
+    "from catflow.metad.fes import FreeEnergySurface\n",
     "\n",
     "# do sum_hills\n",
     "fes = FreeEnergySurface.from_hills(h2, resolution=256)"
@@ -447,7 +447,7 @@
     }
    ],
    "source": [
-    "from catalyner.metad.profile import FreeEnergyProfile\n",
+    "from catflow.metad.profile import FreeEnergyProfile\n",
     "fe_profile = FreeEnergyProfile(fes, h2)\n",
     "fe_profile.plot(energy_unit=\"kJ/mol\", cmap=\"viridis\", style='ticks', context='notebook')"
    ]
@@ -472,7 +472,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#from catalyner.metad.string import StringMethod\n",
+    "#from catflow.metad.string import StringMethod\n",
     "s = StringMethod(fes)"
    ]
   },

docs/gen_ref.py

@@ -4,7 +4,7 @@
 
 nav = mkdocs_gen_files.Nav()
 
-for path in sorted(Path("catalyner").glob("**/*.py")):
+for path in sorted(Path("catflow").glob("**/*.py")):
     module_path = path.relative_to(".").with_suffix("")
     doc_path = path.relative_to(".").with_suffix(".md")
     full_doc_path = Path("reference", doc_path)