scilens 0.1.0__py3-none-any.whl

scilens/run/models/task_results.py

@@ -0,0 +1,5 @@
+_A=None
+from pydantic import BaseModel
+from scilens.processors.models.results import ProcessorResults
+from scilens.report.report import ReportProcessResults
+class TaskResults(BaseModel):error:str|_A=_A;processor_results:ProcessorResults|_A=_A;report_results:ReportProcessResults|_A=_A

scilens/run/models/task_runtime.py

@@ -0,0 +1,2 @@
+from pydantic import BaseModel
+class TaskRuntime(BaseModel):sys:dict[str,str];env:dict[str,str];vars:dict[str,str]

scilens/run/run_task.py

@@ -0,0 +1,41 @@
+import logging,os
+from enum import Enum
+from pydantic import BaseModel
+from scilens.config.models import AppConfig
+from scilens.run.models.task_results import TaskResults
+from scilens.run.models.task_runtime import TaskRuntime
+from scilens.run.task_context import TaskContext
+from scilens.processors.models.results import ProcessorResults
+from scilens.processors import Analyse,Compare,ExecuteAndCompare
+from scilens.report.report import Report
+from scilens.utils.system import info as system_info
+from scilens.utils.time_tracker import TimeTracker
+from scilens.utils.template import template_render_string
+def var_render(value,runtime):return template_render_string(value,runtime.model_dump())
+def runtime_process_vars(config):
+	A=TaskRuntime(sys=system_info(),env=os.environ.copy(),vars={})
+	for(B,C)in config.variables.items():A.vars[B]=var_render(C,A)
+	return A
+def runtime_apply_to_config(runtime,config_model):
+	C=runtime;B=config_model
+	for(D,J)in B.__class__.__pydantic_fields__.items():
+		A=getattr(B,D);E=issubclass(A.__class__,BaseModel);F=isinstance(A.__class__,type)and issubclass(A.__class__,Enum);G=isinstance(A,str);H=isinstance(A,list)and all(isinstance(A,str)for A in A);I=isinstance(A,dict)and all(isinstance(A,str)and isinstance(B,str)for(A,B)in A.items())
+		if E:runtime_apply_to_config(C,A)
+		elif G and not F:setattr(B,D,var_render(A,C))
+		elif H:setattr(B,D,[var_render(A,C)for A in A])
+		elif I:setattr(B,D,{A:var_render(B,C)for(A,B)in A.items()})
+class RunTask:
+	def __init__(A,context):A.context=context
+	def _get_processors(A):return{A.__name__:A for A in[Analyse,Compare,ExecuteAndCompare]}
+	def process(A):
+		logging.info(f"Running task");logging.info(f"Prepare runtime variables");H=runtime_process_vars(A.context.config);logging.info(f"Apply runtime variables to config");runtime_apply_to_config(H,A.context.config);logging.debug(f"on working_dir '{A.context.working_dir}'");logging.debug(f"with origin_working_dir '{A.context.origin_working_dir}'");logging.debug(f"with config {A.context.config.model_dump_json(indent=4)}");C=A.context.config.processor
+		if not C:raise Exception('Processor not defined in config.')
+		D=A._get_processors().get(C)
+		if not D:raise Exception('Processor not found.')
+		logging.info(f"Processor '{D.__name__}'")
+		try:F=TimeTracker();G=D(A.context);E=G.process();F.stop();I=F.get_data()
+		except Exception as B:logging.error(B);return TaskResults(error=str(B))
+		finally:G=None
+		try:J=Report(A.context.working_dir,[A.context.origin_working_dir],A.context.config.report,A.context.task_name).process({'meta':{'system_info':system_info(),'task_info':{'processor':C,'process_time':I}},'processor_results':E.data},C)
+		except Exception as B:logging.error(B);return TaskResults(error=str(B),processor_results=E)
+		return TaskResults(processor_results=E,report_results=J)

scilens/run/standalone_task_runner.py

@@ -0,0 +1,9 @@
+import logging
+from scilens.config.load import config_load
+from scilens.run.task_context import TaskContext
+from scilens.run.run_task import RunTask
+from scilens.config.models import AppConfig
+class StandaloneTaskRunner:
+	config_path=None
+	def __init__(A,config):A.config=config_load(config)
+	def process(A,working_dir,origin_working_dir=None):B=TaskContext(config=A.config,config_file=A.config_path,working_dir=working_dir,origin_working_dir=origin_working_dir);C=RunTask(B);D=C.process();return D

scilens/run/task_context.py

@@ -0,0 +1,12 @@
+import os
+from scilens.config.models import AppConfig
+class TaskContext:
+	working_dir:str;origin_working_dir:str;config:AppConfig;config_file:str|None=None
+	def __init__(A,working_dir,origin_working_dir,config,config_file):
+		E='working_dir must be an absolute path.';D='working_dir does not exist.';C=origin_working_dir;B=working_dir
+		if not os.path.isdir(B):raise Exception(D)
+		if not os.path.isabs(B):raise Exception(E)
+		if not os.path.isdir(C):raise Exception(D)
+		if not os.path.isabs(C):raise Exception(E)
+		A.config=config;A.config_file=config_file;A.working_dir=B;A.origin_working_dir=C;A.task_name=''
+		if len(B)>len(C):A.task_name=B.replace(C,'')

scilens/run/tasks_collector.py

@@ -0,0 +1,52 @@
+_A=None
+import logging,os
+from scilens.app import pkg_name
+from scilens.config.load import config_load
+from scilens.run.task_context import TaskContext
+from scilens.run.run_task import RunTask
+from scilens.utils.file import list_paths_at_depth
+def configfile_search_in_folder(folder):
+	for B in['yml','yaml']:
+		A=f"{folder}/{pkg_name}.{B}"
+		if os.path.isfile(A):return A
+def configfile_search_in_folder_recursive(folder):
+	A=folder;B=[];C=configfile_search_in_folder(A)
+	if C:return[(A,C)]
+	else:
+		D=[os.path.join(A,B)for B in os.listdir(A)if os.path.isdir(os.path.join(A,B))]
+		for dir in D:B+=configfile_search_in_folder_recursive(dir)
+	return B
+class TasksCollector:
+	def __init__(A,absolute_working_dir,config_filepath=_A,collect_discover=False,collect_depth=_A,tags=_A,processor=_A):
+		F=processor;E=collect_discover;D=config_filepath;C=collect_depth;B=absolute_working_dir
+		if not os.path.isdir(B):raise Exception('absolute_working_dir does not exist.')
+		if not os.path.isabs(B):raise Exception('absolute_working_dir must be an absolute path.')
+		A.path=B
+		if not bool(D)+E+(bool(C)or C==0)+bool(F)in[0,1]:raise Exception('config_filepath, collect_discover, collect_depth and processor are mutually exclusive.')
+		A.config_filepath=D;A.collect_discover=E;A.collect_depth=C;A.processor=F;A.tags=tags
+	def process(A,options_path_value):
+		F=options_path_value;logging.info(f"Collecting tasks");B=[]
+		if A.collect_discover:
+			logging.info(f"Collect-discover: Exploring recursively the folder '{A.path}'");H=configfile_search_in_folder_recursive(A.path);logging.info(f"Collect-discover: Number of config files found: {len(H)}");logging.info(f"Loading configurations")
+			for(K,I)in H:E=config_load(I,F);C=TaskContext(config=E,config_file=I,working_dir=K,origin_working_dir=A.path);B.append(RunTask(C))
+		elif A.processor:E=config_load({'processor':A.processor},F);C=TaskContext(config=E,config_file=_A,working_dir=A.path,origin_working_dir=A.path);B.append(RunTask(C))
+		else:
+			D=_A
+			if A.config_filepath:
+				if not os.path.isfile(A.config_filepath):raise Exception(f"Config file '{A.config_filepath}' not found.")
+				else:D=os.path.abspath(A.config_filepath)
+			else:
+				D=configfile_search_in_folder(A.path)
+				if D:logging.info(f"Config file found at '{D}'")
+				else:raise Exception(f"Config file not found in '{A.path}'")
+			E=config_load(D,F)
+			if A.collect_depth is not _A:
+				logging.info(f"Collecting tasks at depth: {A.collect_depth}");J=list_paths_at_depth(A.path,A.collect_depth);logging.info(f"Number of dirs found: {len(J)}")
+				for dir in J:
+					G=configfile_search_in_folder(dir)
+					if G:L=config_load(D,F,config_override=G);C=TaskContext(config=L,config_file=G,working_dir=dir,origin_working_dir=A.path)
+					else:C=TaskContext(config=E,config_file=D,working_dir=dir,origin_working_dir=A.path)
+					B.append(RunTask(C))
+			else:C=TaskContext(config=E,config_file=D,working_dir=A.path,origin_working_dir=A.path);B.append(RunTask(C))
+		if A.tags:logging.info(f"Filtering tasks with tags: {A.tags}");B=[B for B in B if any(A in(B.context.config.tags or[])for A in A.tags)]
+		logging.info(f"Number of tasks collected: {len(B)}");return B

scilens/utils/dict.py

@@ -0,0 +1,6 @@
+from functools import reduce
+def dict_path_set(obj,path,value):
+	A=obj;B=path.split('.')
+	for C in B[:-1]:A=A.setdefault(C,{})
+	A[B[-1]]=value
+def dict_path_get(obj,path):return reduce(dict.get,path.split('.'),obj)

scilens/utils/file.py

@@ -0,0 +1,43 @@
+import json,os,shutil,yaml
+def file_remove(path):
+	if os.path.exists(path):os.remove(path)
+def dir_remove(path):
+	if os.path.exists(path):shutil.rmtree(path)
+def dir_create(path):
+	if not os.path.exists(path):os.makedirs(path)
+def dir_copy(source_dir,target_dir):shutil.copytree(source_dir,target_dir)
+def dir_is_empty(path):return len(os.listdir(path))==0
+def file_copy(source_file,destination_file):A=destination_file;os.makedirs(os.path.dirname(A),exist_ok=True);shutil.copy(source_file,A)
+def copy(src,dst):
+	A=src
+	if os.path.isfile(A):file_copy(A,dst)
+	else:dir_copy(A,dst)
+def text_write(path,data):
+	with open(path,'w')as A:A.write(data)
+def text_append(path,data):
+	with open(path,'a')as A:A.write(data)
+def text_load(path):
+	with open(path,'r')as A:return A.read()
+def json_write(path,data):
+	with open(path,'w')as A:json.dump(data,A,indent=4)
+def json_write_small(path,data):
+	with open(path,'w')as A:json.dump(data,A)
+def json_load(path):
+	with open(path)as A:return json.load(A)
+def yaml_write(path,data):
+	with open(path,'w')as A:yaml.dump(data,A,default_flow_style=False)
+def move(source,target):shutil.move(source,target)
+def list_paths_at_depth(root_dir,depth):
+	B=depth;A=root_dir;C=[]
+	for(D,F,G)in os.walk(A):
+		E=D.count(os.sep)-A.count(os.sep)
+		if E==B:C.append(D)
+		elif E>B:F.clear()
+	return C
+def list_paths_for_file_recursive(path,filename):
+	B=filename;A=path;C=[];D=os.path.join(A,B)
+	if os.path.isfile(D):return[A]
+	else:
+		E=[os.path.join(A,B)for B in os.listdir(A)if os.path.isdir(os.path.join(A,B))]
+		for dir in E:C+=list_paths_for_file_recursive(dir,B)
+	return C

scilens/utils/php.py

@@ -0,0 +1,15 @@
+def dict_to_php_array(data,indent=0):
+	F='array(\n';D=indent;B=data;A='';C=' '*(D*4)
+	if isinstance(B,dict):
+		A+=F
+		for(G,E)in B.items():A+=f"{C}    '{G}' => {dict_to_php_array(E,D+1)},\n"
+		A+=f"{C})"
+	elif isinstance(B,list):
+		A+=F
+		for E in B:A+=f"{C}    {dict_to_php_array(E,D+1)},\n"
+		A+=f"{C})"
+	elif isinstance(B,str):A+=f"'{B}'"
+	elif isinstance(B,bool):A+='true'if B else'false'
+	elif B is None:A+='null'
+	else:A+=str(B)
+	return A

scilens/utils/system.py

@@ -0,0 +1,2 @@
+import platform,sys
+def info():A=sys.version_info;return{'os':platform.system().lower(),'arch':platform.machine(),'python':f"{A.major}.{A.minor}.{A.micro}",'python_info':sys.version}

scilens/utils/template.py

@@ -0,0 +1,5 @@
+from jinja2 import Template,Environment,FileSystemLoader
+def template_render_string(template_str,context):return Template(template_str).render(context)
+def template_render_path(filepath,context):
+	with open(filepath,'r')as A:B=A.read();return template_render_string(B,context)
+def template_render_infolder(filename,context,template_dir):A=FileSystemLoader([template_dir]);B=Environment(loader=A);return B.get_template(filename).render(context)

scilens/utils/time_tracker.py

@@ -0,0 +1,6 @@
+import datetime as dt
+class TimeTracker:
+	def __init__(A):A.start_time=dt.datetime.now(dt.timezone.utc);A.end_time=None
+	def stop(A):A.end_time=dt.datetime.now(dt.timezone.utc)
+	def get_datetime_data(B,datetime):A=datetime;return{'datetime':A.strftime('%Y-%m-%d %H:%M:%S'),'date':A.strftime('%Y-%m-%d'),'time':A.strftime('%H:%M:%S')}
+	def get_data(A):return{'start':A.get_datetime_data(A.start_time),'end':A.get_datetime_data(A.end_time)if A.end_time else None,'duration_seconds':(A.end_time-A.start_time).total_seconds()if A.end_time else None}

scilens/utils/vectors.py

@@ -0,0 +1,4 @@
+def min_max_scaling(vector):
+	A=vector;B=min(A);C=max(A)
+	if C==B:return
+	return[(A-B)/(C-B)for A in A]

scilens/utils/web.py

@@ -0,0 +1,20 @@
+import requests
+from urllib.parse import urlparse
+BASE_HEADERS={'User-Agent':'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36'}
+class Web:
+	def download(E,url,filename,headers=None):
+		A=headers;B=BASE_HEADERS.copy()
+		if A:B.update(A)
+		C=requests.get(url,headers=B);C.raise_for_status()
+		with open(filename,'wb')as D:D.write(C.content)
+	def download_progress(L,url,filename,headers=None,callback100=None):
+		D=callback100;C=headers;E=BASE_HEADERS.copy()
+		if C:E.update(C)
+		F=requests.get(url,headers=E,stream=True);I=int(F.headers.get('Content-Length',0));G=0;J=I//100;A=0
+		with open(filename,'wb')as K:
+			for B in F.iter_content(chunk_size=1024):
+				if B:
+					K.write(B);G+=len(B);H=G//J
+					if H>A:
+						A=H
+						if D:D(A)

scilens-0.1.0.dist-info/METADATA

@@ -0,0 +1,44 @@
+Metadata-Version: 2.1
+Name: scilens
+Version: 0.1.0
+Summary: A CesGensLaB framework for data collecting and deep analysis
+Home-page: https://scilens.dev
+License: Proprietary
+Author: CesGensLaB
+Author-email: contact@cesgenlab.fr
+Requires-Python: >=3.10,<4.0
+Classifier: License :: Other/Proprietary License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: coloredlogs (>=15.0.1,<16.0.0)
+Requires-Dist: jinja2 (>=3.1.4,<4.0.0)
+Requires-Dist: pydantic (>=2.10.2,<3.0.0)
+Requires-Dist: pyyaml (>=6.0.2,<7.0.0)
+Requires-Dist: requests (>=2.32.3,<3.0.0)
+Requires-Dist: rich-click (>=1.8.4,<2.0.0)
+Project-URL: Documentation, https://scilens.dev/docs
+Description-Content-Type: text/markdown
+
+# SciLens
+
+![](https://media.cesgenslab.fr/cglb-logo/lens_v0_name.png)
+
+A [CesGensLaB](https://cesgenslab.fr) framework for **data collecting** and **data deep analysis**.
+
+**Resources:**
+
+- [Homepage](https://scilens.dev)
+
+- [Documentation](https://scilens.dev/docs)
+
+- [License](https://scilens.dev/legal/license)
+
+- [Demos](https://github.com/CesGensLaB/scilens-demos)
+
+- [Issue Tracker](https://forge-02.cesgenslab.cloud/cglb-registry/scilens-issues/issues)
+
+
+

scilens-0.1.0.dist-info/RECORD

@@ -0,0 +1,95 @@
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+scilens/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+scilens/cli/cglb.py,sha256=R0377H5H193DJ_h4hj32m6qvrZrMnSFOxSGVl2FItiU,443
+scilens/cli/config.py,sha256=XVY6q5E9fb6MZzPct4-X7m6e45erpt5MCIuzKTBKPAI,965
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