start hadrons intergration

.gitignore

@@ -1,4 +1,3 @@
 pyerrors_corrlib.egg-info
 __pycache__
-*.egg-info
-test.ipynb
+*.egg-info

corrlib/find.py

@@ -5,7 +5,7 @@ import json
 import pandas as pd
 import numpy as np
 from .input.implementations import codes
-from .tools import k2m, get_file
+from .tools import k2m
 # this will implement the search functionality
 
 
@@ -143,22 +143,21 @@ def find_record(path, ensemble, correlator_name, code, project=None, parameters=
     db = path + '/backlogger.db'
     if code not in codes:
         raise ValueError("Code " + code + "unknown, take one of the following:" + ", ".join(codes))
-    get_file(path, "backlogger.db")
+    if os.path.exists(db):
+        dl.get(db, dataset=path)
     results = _db_lookup(db, ensemble, correlator_name,code, project, parameters=parameters, created_before=created_before, created_after=created_after, updated_before=updated_before, updated_after=updated_after, revision=revision)
     if code == "sfcf":
         results = sfcf_filter(results, **kwargs)
-    print("Found " + str(len(results)) + " result" + ("s" if len(results)>1 else ""))
+    print("Found " + str(len(results)) + " results")
     return results.reset_index()
 
 
-def find_project(path, name):
-    get_file(path, "backlogger.db")
-    return _project_lookup_by_alias(os.path.join(path, "backlogger.db"), name)
+def find_project(db, name):
+    return _project_lookup_by_alias(db, name)
 
 
 def list_projects(path):
     db = path + '/backlogger.db'
-    get_file(path, "backlogger.db")
     conn = sqlite3.connect(db)
     c = conn.cursor()
     c.execute("SELECT id,aliases FROM projects")

corrlib/input/hadrons.py

@@ -0,0 +1,48 @@
+import pyerrors.input.hadrons as input
+import datalad.api as dl
+import os
+
+# same as in Grid/qcd/spin/Gamma.h
+
+defd_gammas=[
+            'MinusGamma5', 'Gamma5',
+            'MinusGammaT', 'GammaT', 'MinusGammaTGamma5', 'GammaTGamma5',
+            'MinusGammaX', 'GammaX', 'MinusGammaXGamma5', 'GammaXGamma5',
+            'MinusGammaY', 'GammaY', 'MinusGammaYGamma5', 'GammaYGamma5',
+            'MinusGammaZ', 'GammaZ', 'MinusGammaZGamma5', 'GammaZGamma5',
+            'MinusIdentity', 'Identity',
+            'MinusSigmaXT', 'SigmaXT',
+            'MinusSigmaXY', 'SigmaXY',
+            'MinusSigmaXZ', 'SigmaXZ',
+            'MinusSigmaYT', 'SigmaYT',
+            'MinusSigmaYZ', 'SigmaYZ',
+            'MinusSigmaZT', 'SigmaZT'
+            ]
+
+
+def read_meson_hd5(path, project, dir_in_project, prefix, ensemble, gammas):
+    directory = os.path.join(path, "projects", project, dir_in_project)
+    measurements = {}
+
+    dl.get(directory, dataset=path)
+
+    if gammas == 'all':
+        for g1 in defd_gammas:
+            for g2 in defd_gammas:
+                try:
+                    corr = input.read_meson_hd5(directory, prefix, ensemble, (g1, g2))
+                    measurements[g1][g2] = corr
+                except Exception:
+                    raise Exception("Combination (" + g1 + "," + g2 + ") not in data.")
+    else:
+        for gs in gammas:
+            if len(gs) == 2:
+                if gs[0] not in defd_gammas:
+                    raise ValueError(gammas[0] + " is none of the defined gammas.")
+                if gs[1] not in defd_gammas:
+                    raise ValueError(gammas[1] + " is none of the defined gammas.")
+                corr = input.read_meson_hd5(directory, prefix, ensemble, gs)
+                measurements[gs[0]][gs[1]] = corr
+            else:
+                raise Exception("Each element in 'gammas' has to have length 2.")
+    return measurements

corrlib/main.py

@@ -5,7 +5,7 @@ import os
 from .git_tools import move_submodule
 import shutil
 from .find import _project_lookup_by_id
-from .tools import list2str, str2list, get_file
+from .tools import list2str, str2list
 from typing import Union
 
 
@@ -24,15 +24,13 @@ def create_project(path: str, uuid: str, owner: Union[str, None]=None, tags: Uni
     code: str (optional)
         The code that was used to create the measurements.
     """
-    db = path + "/backlogger.db"
-    get_file(path, "backlogger.db")
-    conn = sqlite3.connect(db)
+    conn = sqlite3.connect(path + "/backlogger.db")
     c = conn.cursor()
     known_projects = c.execute("SELECT * FROM projects WHERE id=?", (uuid,))
     if known_projects.fetchone():
         raise ValueError("Project already imported, use update_project() instead.")
 
-    dl.unlock(db, dataset=path)
+    dl.unlock(path + "/backlogger.db", dataset=path)
     alias_str = None
     if aliases is not None:
         alias_str = list2str(aliases)
@@ -42,12 +40,11 @@ def create_project(path: str, uuid: str, owner: Union[str, None]=None, tags: Uni
     c.execute("INSERT INTO projects (id, aliases, customTags, owner, code, created_at, updated_at) VALUES (?, ?, ?, ?, ?, datetime('now'), datetime('now'))", (uuid, alias_str, tag_str, owner, code))
     conn.commit()
     conn.close()
-    dl.save(db, message="Added entry for project " + uuid + " to database", dataset=path)
+    dl.save(path + "/backlogger.db", message="Added entry for project " + uuid + " to database", dataset=path)
 
 
-def update_project_data(path, uuid, prop, value = None):
-    get_file(path, "backlogger.db")
-    conn = sqlite3.connect(os.path.join(path, "backlogger.db"))
+def update_project_data(db, uuid, prop, value = None):
+    conn = sqlite3.connect(db)
     c = conn.cursor()
     c.execute(f"UPDATE projects SET '{prop}' = '{value}' WHERE id == '{uuid}'")
     conn.commit()
@@ -57,7 +54,6 @@ def update_project_data(path, uuid, prop, value = None):
 
 def update_aliases(path: str, uuid: str, aliases: list[str]):
     db = os.path.join(path, "backlogger.db")
-    get_file(path, "backlogger.db")
     known_data = _project_lookup_by_id(db, uuid)[0]
     known_aliases = known_data[1]
 
@@ -77,7 +73,7 @@ def update_aliases(path: str, uuid: str, aliases: list[str]):
     if not len(new_alias_list) == len(known_alias_list):
         alias_str = list2str(new_alias_list)
         dl.unlock(db, dataset=path)
-        update_project_data(path, uuid, "aliases", alias_str)
+        update_project_data(db, uuid, "aliases", alias_str)
         dl.save(db, dataset=path)
     return
 
@@ -121,13 +117,11 @@ def import_project(path: str, url: str, owner: Union[str, None]=None, tags: Unio
     if not uuid:
         raise ValueError("The dataset does not have a uuid!")
     if not os.path.exists(path + "/projects/" + uuid):
-        db = path + "/backlogger.db"
-        get_file(path, "backlogger.db")
-        dl.unlock(db, dataset=path)
+        dl.unlock(path + "/backlogger.db", dataset=path)
         create_project(path, uuid, owner, tags, aliases, code)
         move_submodule(path, 'projects/tmp', 'projects/' + uuid)
         os.mkdir(path + '/import_scripts/' + uuid)
-        dl.save([db, path + '/projects/' + uuid], message="Import project from " + url, dataset=path)
+        dl.save([path + "/backlogger.db", path + '/projects/' + uuid], message="Import project from " + url, dataset=path)
     else:
         dl.drop(tmp_path, reckless='kill')
         shutil.rmtree(tmp_path)    
@@ -140,11 +134,3 @@ def import_project(path: str, url: str, owner: Union[str, None]=None, tags: Unio
             
     # make this more concrete
     return uuid
-
-
-def drop_project_data(path: str, uuid: str, path_in_project: str = ""):
-    """
-    Drop (parts of) a prject to free up diskspace
-    """
-    dl.drop(path + "/projects/" + uuid + "/" + path_in_project)
-

corrlib/meas_io.py

@@ -7,7 +7,7 @@ import json
 from typing import Union
 from pyerrors import Obs, Corr, dump_object, load_object
 from hashlib import sha256
-from .tools import cached, get_file
+from .tools import cached
 import shutil
 
 
@@ -28,7 +28,6 @@ def write_measurement(path, ensemble, measurement, uuid, code, parameter_file=No
         The uuid of the project.
     """
     db = os.path.join(path, 'backlogger.db')
-    get_file(path, "backlogger.db")
     dl.unlock(db, dataset=path)
     conn = sqlite3.connect(db)
     c = conn.cursor()
@@ -168,9 +167,8 @@ def cache_path(path, file, key):
 
 
 def preload(path: str, file: str):
-    get_file(path, file)
+    dl.get(os.path.join(path, file), dataset=path)
     filedict = pj.load_json_dict(os.path.join(path, file))
-    print("> read file")
     return filedict
 
 
@@ -178,7 +176,6 @@ def drop_record(path: str, meas_path: str):
     file_in_archive = meas_path.split("::")[0]
     file = os.path.join(path, file_in_archive)
     db = os.path.join(path, 'backlogger.db')
-    get_file(path, 'backlogger.db')
     sub_key = meas_path.split("::")[1]
     dl.unlock(db, dataset=path)
     conn = sqlite3.connect(db)

corrlib/tools.py

@@ -1,5 +1,4 @@
-import os
-import datalad.api as dl
+
 
 
 def str2list(string):
@@ -17,13 +16,3 @@ def m2k(m):
 
 def k2m(k):
     return (1/(2*k))-4
-
-
-def get_file(path, file):
-    if file == "backlogger.db":
-        print("Downloading database...")
-    else:
-        print("Downloading data...")
-    dl.get(os.path.join(path, file), dataset=path)
-    print("> downloaded file")
-    

corrlib/version.py

@@ -1 +1 @@
-__version__ = "0.2.3"
+__version__ = "0.1.4"

examples/example_import.toml

@@ -1,28 +0,0 @@
-['project']
-url = "git@kuhl-mann.de:lattice/cA_data.git"
-code = "sfcf"
-[measurements]
-[measurements.a]
-    path = "/path/to/measurement"
-    ensemble = "A1k1"
-    param_file = "/path/to/file"
-    version = "1.1"
-    prefix = "pref"
-    cfg_seperator = "n"
-    names = ['list', 'of', 'names']
-[measurements.b]
-    path = "/path/to/measurement"
-    ensemble = "A1k1"
-    param_file = "/path/to/file"
-    version = "1.1"
-    prefix = "pref"
-    cfg_seperator = "n"
-    names = ['list', 'of', 'names']
-[measurements.c]
-    path = "/path/to/measurement"
-    ensemble = "A1k1"
-    param_file = "/path/to/file"
-    version = "1.1"
-    prefix = "pref"
-    cfg_seperator = "n"
-    names = ['list', 'of', 'names']

projects/tmp

@@ -0,0 +1 @@
+Subproject commit 216fe4ed3467ed486390735f8072856cf3d0a409

pyproject.toml

@@ -1,6 +0,0 @@
-[build-system]
-requires = ["setuptools >= 63.0.0", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[tool.ruff.lint]
-ignore = ["F403"]

tests/import_project_test.py

@@ -1,17 +0,0 @@
-import corrlib.toml as t
-
-
-def test_toml_check_measurement_data():
-    measurements = {
-                    "a":
-                        {
-                            "path": "/path/to/measurement",
-                            "ensemble": "A1k1",
-                            "param_file": "/path/to/file",
-                            "version": "1.1",
-                            "prefix": "pref",
-                            "cfg_seperator": "n",
-                            "names": ['list', 'of', 'names']
-                        }
-                    }
-    t.check_measurement_data(measurements)