chore(deps): update dependency scipy to v1.10.1

Reviewed-on: #21

.gitignore

@@ -114,6 +114,10 @@ ENV/
 env.bak/
 venv.bak/
 
+# direnv
+.envrc
+.direnv
+
 # Spyder project settings
 .spyderproject
 .spyproject

CHANGELOG.md

@@ -2,6 +2,35 @@
 
 All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines.
 
+### [0.6.4](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.3...0.6.4) (2022-08-13)
+
+
+### Features
+
+* Prints model names while running ([7ea1d71](https://gitea.deepak.science:2222/physics/deepdog/commit/7ea1d715f67e81c9fa841c5a62f1cc700ff7363d))
+
+### [0.6.3](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.2...0.6.3) (2022-06-12)
+
+
+### Features
+
+* adds fast filter variant ([2c5c122](https://gitea.deepak.science:2222/physics/deepdog/commit/2c5c1228209e51d17253f07470e2f1e6dc6872d7))
+* adds tester for fast filter real spectrum ([0a1a277](https://gitea.deepak.science:2222/physics/deepdog/commit/0a1a27759b0d4ab01da214b76ab14bf2b1fe00e3))
+
+### [0.6.2](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.1...0.6.2) (2022-05-26)
+
+
+### Features
+
+* adds better import api for real data run ([d7e0f13](https://gitea.deepak.science:2222/physics/deepdog/commit/d7e0f13ca55197b24cb534c80f321ee76b9c4a40))
+
+### [0.6.1](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.0...0.6.1) (2022-05-22)
+
+
+### Features
+
+* adds new runner for real spectra ([bd56f24](https://gitea.deepak.science:2222/physics/deepdog/commit/bd56f247748babb2ee1f2a1182d25aa968bff5a5))
+
 ## [0.6.0](https://gitea.deepak.science:2222/physics/deepdog/compare/0.5.0...0.6.0) (2022-05-22)
 
 

deepdog/__init__.py

@@ -2,6 +2,7 @@ import logging
 from deepdog.meta import __version__
 from deepdog.bayes_run import BayesRun
 from deepdog.bayes_run_simulpairs import BayesRunSimulPairs
+from deepdog.real_spectrum_run import RealSpectrumRun
 
 
 def get_version():
@@ -12,6 +13,7 @@ __all__ = [
 	"get_version",
 	"BayesRun",
 	"BayesRunSimulPairs",
+	"RealSpectrumRun",
 ]
 
 

deepdog/real_spectrum_run.py

@@ -0,0 +1,222 @@
+import pdme.inputs
+import pdme.model
+import pdme.measurement
+import pdme.measurement.input_types
+import pdme.measurement.oscillating_dipole
+import pdme.util.fast_v_calc
+import pdme.util.fast_nonlocal_spectrum
+from typing import Sequence, Tuple, List, Dict, Union
+import datetime
+import csv
+import multiprocessing
+import logging
+import numpy
+
+
+# TODO: remove hardcode
+CHUNKSIZE = 50
+
+
+_logger = logging.getLogger(__name__)
+
+
+def get_a_result(input) -> int:
+	model, dot_inputs, lows, highs, monte_carlo_count, seed = input
+
+	rng = numpy.random.default_rng(seed)
+	# TODO: A long term refactor is to pull the frequency stuff out from here. The None stands for max_frequency, which is unneeded in the actually useful models.
+	sample_dipoles = model.get_monte_carlo_dipole_inputs(
+		monte_carlo_count, None, rng_to_use=rng
+	)
+	vals = pdme.util.fast_v_calc.fast_vs_for_dipoleses(dot_inputs, sample_dipoles)
+	return numpy.count_nonzero(pdme.util.fast_v_calc.between(vals, lows, highs))
+
+
+def get_a_result_fast_filter(input) -> int:
+	model, dot_inputs, lows, highs, monte_carlo_count, seed = input
+
+	rng = numpy.random.default_rng(seed)
+	# TODO: A long term refactor is to pull the frequency stuff out from here. The None stands for max_frequency, which is unneeded in the actually useful models.
+	sample_dipoles = model.get_monte_carlo_dipole_inputs(
+		monte_carlo_count, None, rng_to_use=rng
+	)
+
+	current_sample = sample_dipoles
+	for di, low, high in zip(dot_inputs, lows, highs):
+
+		if len(current_sample) < 1:
+			break
+		vals = pdme.util.fast_v_calc.fast_vs_for_dipoleses(
+			numpy.array([di]), current_sample
+		)
+
+		current_sample = current_sample[numpy.all((vals > low) & (vals < high), axis=1)]
+	return len(current_sample)
+
+
+class RealSpectrumRun:
+	"""
+	A bayes run given some real data.
+
+	Parameters
+	----------
+	measurements : Sequence[pdme.measurement.DotRangeMeasurement]
+	The dot inputs for this bayes run.
+
+	models_with_names : Sequence[Tuple(str, pdme.model.DipoleModel)]
+	The models to evaluate.
+
+	actual_model : pdme.model.DipoleModel
+	The model which is actually correct.
+
+	filename_slug : str
+	The filename slug to include.
+
+	run_count: int
+	The number of runs to do.
+	"""
+
+	def __init__(
+		self,
+		measurements: Sequence[pdme.measurement.DotRangeMeasurement],
+		models_with_names: Sequence[Tuple[str, pdme.model.DipoleModel]],
+		filename_slug: str,
+		monte_carlo_count: int = 10000,
+		monte_carlo_cycles: int = 10,
+		target_success: int = 100,
+		max_monte_carlo_cycles_steps: int = 10,
+		chunksize: int = CHUNKSIZE,
+		initial_seed: int = 12345,
+		use_fast_filter: bool = True,
+	) -> None:
+		self.measurements = measurements
+		self.dot_inputs = [(measure.r, measure.f) for measure in self.measurements]
+
+		self.dot_inputs_array = pdme.measurement.input_types.dot_inputs_to_array(
+			self.dot_inputs
+		)
+
+		self.models = [model for (_, model) in models_with_names]
+		self.model_names = [name for (name, _) in models_with_names]
+		self.model_count = len(self.models)
+
+		self.monte_carlo_count = monte_carlo_count
+		self.monte_carlo_cycles = monte_carlo_cycles
+		self.target_success = target_success
+		self.max_monte_carlo_cycles_steps = max_monte_carlo_cycles_steps
+
+		self.csv_fields = []
+
+		self.compensate_zeros = True
+		self.chunksize = chunksize
+		for name in self.model_names:
+			self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"])
+
+		# for now initialise priors as uniform.
+		self.probabilities = [1 / self.model_count] * self.model_count
+
+		timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
+		self.use_fast_filter = use_fast_filter
+		ff_string = "no_fast_filter"
+		if self.use_fast_filter:
+			ff_string = "fast_filter"
+		self.filename = f"{timestamp}-{filename_slug}.realdata.{ff_string}.bayesrun.csv"
+		self.initial_seed = initial_seed
+
+	def go(self) -> None:
+		with open(self.filename, "a", newline="") as outfile:
+			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
+			writer.writeheader()
+
+		(
+			lows,
+			highs,
+		) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
+			self.measurements
+		)
+
+		# define a new seed sequence for each run
+		seed_sequence = numpy.random.SeedSequence(self.initial_seed)
+
+		results = []
+		_logger.debug("Going to iterate over models now")
+		for model_count, (model, model_name) in enumerate(
+			zip(self.models, self.model_names)
+		):
+			_logger.debug(f"Doing model #{model_count}: {model_name}")
+			core_count = multiprocessing.cpu_count() - 1 or 1
+			with multiprocessing.Pool(core_count) as pool:
+				cycle_count = 0
+				cycle_success = 0
+				cycles = 0
+				while (cycles < self.max_monte_carlo_cycles_steps) and (
+					cycle_success <= self.target_success
+				):
+					_logger.debug(f"Starting cycle {cycles}")
+					cycles += 1
+					current_success = 0
+					cycle_count += self.monte_carlo_count * self.monte_carlo_cycles
+
+					# generate a seed from the sequence for each core.
+					# note this needs to be inside the loop for monte carlo cycle steps!
+					# that way we get more stuff.
+					seeds = seed_sequence.spawn(self.monte_carlo_cycles)
+
+					if self.use_fast_filter:
+						result_func = get_a_result_fast_filter
+					else:
+						result_func = get_a_result
+					current_success = sum(
+						pool.imap_unordered(
+							result_func,
+							[
+								(
+									model,
+									self.dot_inputs_array,
+									lows,
+									highs,
+									self.monte_carlo_count,
+									seed,
+								)
+								for seed in seeds
+							],
+							self.chunksize,
+						)
+					)
+
+					cycle_success += current_success
+					_logger.debug(f"current running successes: {cycle_success}")
+				results.append((cycle_count, cycle_success))
+
+		_logger.debug("Done, constructing output now")
+		row: Dict[str, Union[int, float, str]] = {}
+
+		successes: List[float] = []
+		counts: List[int] = []
+		for model_index, (name, (count, result)) in enumerate(
+			zip(self.model_names, results)
+		):
+
+			row[f"{name}_success"] = result
+			row[f"{name}_count"] = count
+			successes.append(max(result, 0.5))
+			counts.append(count)
+
+		success_weight = sum(
+			[
+				(succ / count) * prob
+				for succ, count, prob in zip(successes, counts, self.probabilities)
+			]
+		)
+		new_probabilities = [
+			(succ / count) * old_prob / success_weight
+			for succ, count, old_prob in zip(successes, counts, self.probabilities)
+		]
+		self.probabilities = new_probabilities
+		for name, probability in zip(self.model_names, self.probabilities):
+			row[f"{name}_prob"] = probability
+		_logger.info(row)
+
+		with open(self.filename, "a", newline="") as outfile:
+			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
+			writer.writerow(row)

flake.lock

@@ -0,0 +1,95 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "locked": {
+        "lastModified": 1648297722,
+        "narHash": "sha256-W+qlPsiZd8F3XkzXOzAoR+mpFqzm3ekQkJNa+PIh1BQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "0f8662f1319ad6abf89b3380dd2722369fc51ade",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "0f8662f1319ad6abf89b3380dd2722369fc51ade",
+        "type": "github"
+      }
+    },
+    "flake-utils_2": {
+      "locked": {
+        "lastModified": 1653893745,
+        "narHash": "sha256-0jntwV3Z8//YwuOjzhV2sgJJPt+HY6KhU7VZUL0fKZQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "1ed9fb1935d260de5fe1c2f7ee0ebaae17ed2fa1",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1655087213,
+        "narHash": "sha256-4R5oQ+OwGAAcXWYrxC4gFMTUSstGxaN8kN7e8hkum/8=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "37b6b161e536fddca54424cf80662bce735bdd1e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "37b6b161e536fddca54424cf80662bce735bdd1e",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1655046959,
+        "narHash": "sha256-gxqHZKq1ReLDe6ZMJSbmSZlLY95DsVq5o6jQihhzvmw=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "07bf3d25ce1da3bee6703657e6a787a4c6cdcea9",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "poetry2nix": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nixpkgs": "nixpkgs_2"
+      },
+      "locked": {
+        "lastModified": 1654921554,
+        "narHash": "sha256-hkfMdQAHSwLWlg0sBVvgrQdIiBP45U1/ktmFpY4g2Mo=",
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "7b71679fa7df00e1678fc3f1d1d4f5f372341b63",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "7b71679fa7df00e1678fc3f1d1d4f5f372341b63",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs",
+        "poetry2nix": "poetry2nix"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

flake.nix

@@ -0,0 +1,63 @@
+{
+  description = "Application packaged using poetry2nix";
+
+  inputs.flake-utils.url = "github:numtide/flake-utils?rev=0f8662f1319ad6abf89b3380dd2722369fc51ade";
+  inputs.nixpkgs.url = "github:NixOS/nixpkgs?rev=37b6b161e536fddca54424cf80662bce735bdd1e";
+  inputs.poetry2nix.url = "github:nix-community/poetry2nix?rev=7b71679fa7df00e1678fc3f1d1d4f5f372341b63";
+
+  outputs = { self, nixpkgs, flake-utils, poetry2nix }:
+    {
+      # Nixpkgs overlay providing the application
+      overlay = nixpkgs.lib.composeManyExtensions [
+        poetry2nix.overlay
+        (final: prev: {
+          # The application
+          deepdog = prev.poetry2nix.mkPoetryApplication {
+            overrides = final.poetry2nix.overrides.withDefaults (self: super: {
+              # …
+              # workaround https://github.com/nix-community/poetry2nix/issues/568
+              pdme = super.pdme.overridePythonAttrs (old: {
+                buildInputs = old.buildInputs or [ ] ++ [ final.python39.pkgs.poetry-core ];
+              });
+            });
+            projectDir = ./.;
+          };
+          deepdogEnv = prev.poetry2nix.mkPoetryEnv {
+            overrides = final.poetry2nix.overrides.withDefaults (self: super: {
+              # …
+              # workaround https://github.com/nix-community/poetry2nix/issues/568
+              pdme = super.pdme.overridePythonAttrs (old: {
+                buildInputs = old.buildInputs or [ ] ++ [ final.python39.pkgs.poetry-core ];
+              });
+            });
+            projectDir = ./.;
+          };
+        })
+      ];
+    } // (flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs {
+          inherit system;
+          overlays = [ self.overlay ];
+        };
+      in
+      {
+        apps = {
+          deepdog = pkgs.deepdog;
+        };
+
+        defaultApp = pkgs.deepdog;
+        devShell = pkgs.mkShell {
+          buildInputs = [
+            pkgs.poetry
+            pkgs.deepdogEnv
+            pkgs.deepdog
+          ];
+          shellHook = ''
+            export DO_NIX_CUSTOM=1
+          '';
+          packages = [ pkgs.nodejs-16_x ];
+        };
+
+      }));
+}

poetry.lock

@@ -44,24 +44,27 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "bleach"
-version = "4.1.0"
+version = "5.0.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
-packaging = "*"
 six = ">=1.9.0"
 webencodings = "*"
 
+[package.extras]
+css = ["tinycss2 (>=1.1.0)"]
+dev = ["pip-tools (==6.5.1)", "pytest (==7.1.1)", "flake8 (==4.0.1)", "tox (==3.24.5)", "sphinx (==4.3.2)", "twine (==4.0.0)", "wheel (==0.37.1)", "hashin (==0.17.0)", "black (==22.3.0)", "mypy (==0.942)"]
+
 [[package]]
 name = "certifi"
-version = "2021.10.8"
+version = "2022.5.18.1"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "cffi"
@@ -87,18 +90,18 @@ unicode_backport = ["unicodedata2"]
 
 [[package]]
 name = "click"
-version = "8.0.3"
+version = "8.1.3"
 description = "Composable command line interface toolkit"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [[package]]
 name = "click-log"
-version = "0.3.2"
+version = "0.4.0"
 description = "Logging integration for Click"
 category = "dev"
 optional = false
@@ -117,21 +120,21 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "coverage"
-version = "6.3.2"
+version = "6.4.2"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-tomli = {version = "*", optional = true, markers = "extra == \"toml\""}
+tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
 
 [package.extras]
 toml = ["tomli"]
 
 [[package]]
 name = "cryptography"
-version = "36.0.1"
+version = "37.0.2"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 category = "dev"
 optional = false
@@ -146,7 +149,7 @@ docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling
 pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"]
 sdist = ["setuptools_rust (>=0.11.4)"]
 ssh = ["bcrypt (>=3.1.5)"]
-test = ["pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"]
+test = ["pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"]
 
 [[package]]
 name = "docutils"
@@ -193,7 +196,7 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.26"
+version = "3.1.27"
 description = "GitPython is a python library used to interact with Git repositories"
 category = "dev"
 optional = false
@@ -212,7 +215,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "importlib-metadata"
-version = "4.11.0"
+version = "4.11.4"
 description = "Read metadata from Python packages"
 category = "dev"
 optional = false
@@ -222,9 +225,9 @@ python-versions = ">=3.7"
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
 perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "iniconfig"
@@ -236,7 +239,7 @@ python-versions = "*"
 
 [[package]]
 name = "invoke"
-version = "1.6.0"
+version = "1.7.1"
 description = "Pythonic task execution"
 category = "dev"
 optional = false
@@ -244,33 +247,33 @@ python-versions = "*"
 
 [[package]]
 name = "jeepney"
-version = "0.7.1"
+version = "0.8.0"
 description = "Low-level, pure Python DBus protocol wrapper."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
-test = ["pytest", "pytest-trio", "pytest-asyncio", "testpath", "trio", "async-timeout"]
+test = ["pytest", "pytest-trio", "pytest-asyncio (>=0.17)", "testpath", "trio", "async-timeout"]
 trio = ["trio", "async-generator"]
 
 [[package]]
 name = "keyring"
-version = "23.5.0"
+version = "23.6.0"
 description = "Store and access your passwords safely."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-importlib-metadata = ">=3.6"
+importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
 jeepney = {version = ">=0.4.2", markers = "sys_platform == \"linux\""}
 pywin32-ctypes = {version = "<0.1.0 || >0.1.0,<0.1.1 || >0.1.1", markers = "sys_platform == \"win32\""}
 SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
 
 [[package]]
 name = "mccabe"
@@ -282,7 +285,7 @@ python-versions = "*"
 
 [[package]]
 name = "mypy"
-version = "0.950"
+version = "0.971"
 description = "Optional static typing for Python"
 category = "dev"
 optional = false
@@ -335,7 +338,7 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [[package]]
 name = "pdme"
-version = "0.8.2"
+version = "0.8.6"
 description = "Python dipole model evaluator"
 category = "main"
 optional = false
@@ -347,26 +350,26 @@ scipy = ">=1.8,<1.9"
 
 [[package]]
 name = "pkginfo"
-version = "1.8.2"
+version = "1.8.3"
 description = "Query metadatdata from sdists / bdists / installed packages."
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 
 [package.extras]
-testing = ["coverage", "nose"]
+testing = ["nose", "coverage"]
 
 [[package]]
 name = "platformdirs"
-version = "2.5.1"
+version = "2.5.2"
 description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
-test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
+docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
+test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
 
 [[package]]
 name = "pluggy"
@@ -414,30 +417,30 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pygments"
-version = "2.11.2"
+version = "2.12.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 
 [[package]]
 name = "pyparsing"
-version = "3.0.7"
-description = "Python parsing module"
+version = "3.0.9"
+description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.6.8"
 
 [package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
+diagrams = ["railroad-diagrams", "jinja2"]
 
 [[package]]
 name = "pytest"
-version = "6.2.5"
+version = "7.1.2"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
@@ -447,10 +450,10 @@ iniconfig = "*"
 packaging = "*"
 pluggy = ">=0.12,<2.0"
 py = ">=1.8.2"
-toml = "*"
+tomli = ">=1.0.0"
 
 [package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
+testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
@@ -469,23 +472,23 @@ testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtuale
 
 [[package]]
 name = "python-gitlab"
-version = "2.10.1"
+version = "3.5.0"
 description = "Interact with GitLab API"
 category = "dev"
 optional = false
-python-versions = ">=3.6.0"
+python-versions = ">=3.7.0"
 
 [package.dependencies]
 requests = ">=2.25.0"
 requests-toolbelt = ">=0.9.1"
 
 [package.extras]
-autocompletion = ["argcomplete (>=1.10.0,<2)"]
+autocompletion = ["argcomplete (>=1.10.0,<3)"]
 yaml = ["PyYaml (>=5.2)"]
 
 [[package]]
 name = "python-semantic-release"
-version = "7.24.0"
+version = "7.29.1"
 description = "Automatic Semantic Versioning for Python projects"
 category = "dev"
 optional = false
@@ -497,15 +500,15 @@ click-log = ">=0.3,<1"
 dotty-dict = ">=1.3.0,<2"
 gitpython = ">=3.0.8,<4"
 invoke = ">=1.4.1,<2"
-python-gitlab = ">=1.10,<3"
+python-gitlab = ">=2,<4"
 requests = ">=2.25,<3"
 semver = ">=2.10,<3"
-tomlkit = "0.7.0"
+tomlkit = ">=0.10.0,<0.11.0"
 twine = ">=3,<4"
 
 [package.extras]
 dev = ["tox", "isort", "black"]
-docs = ["Sphinx (==1.3.6)"]
+docs = ["Sphinx (==1.3.6)", "Jinja2 (==3.0.3)"]
 mypy = ["mypy", "types-requests"]
 test = ["coverage (>=5,<6)", "pytest (>=5,<6)", "pytest-xdist (>=1,<2)", "pytest-mock (>=2,<3)", "responses (==0.13.3)", "mock (==1.3.0)"]
 
@@ -519,11 +522,11 @@ python-versions = "*"
 
 [[package]]
 name = "readme-renderer"
-version = "32.0"
+version = "35.0"
 description = "readme_renderer is a library for rendering \"readme\" descriptions for Warehouse"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 bleach = ">=2.1.0"
@@ -531,24 +534,24 @@ docutils = ">=0.13.1"
 Pygments = ">=2.5.1"
 
 [package.extras]
-md = ["cmarkgfm (>=0.5.0,<0.7.0)"]
+md = ["cmarkgfm (>=0.8.0)"]
 
 [[package]]
 name = "requests"
-version = "2.27.1"
+version = "2.28.0"
 description = "Python HTTP for Humans."
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.7, <4"
 
 [package.dependencies]
 certifi = ">=2017.4.17"
-charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""}
-idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""}
+charset-normalizer = ">=2.0.0,<2.1.0"
+idna = ">=2.5,<4"
 urllib3 = ">=1.21.1,<1.27"
 
 [package.extras]
-socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
+socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
 
 [[package]]
@@ -586,7 +589,7 @@ numpy = ">=1.17.3,<1.25.0"
 
 [[package]]
 name = "secretstorage"
-version = "3.3.1"
+version = "3.3.2"
 description = "Python bindings to FreeDesktop.org Secret Service API"
 category = "dev"
 optional = false
@@ -636,17 +639,9 @@ category = "dev"
 optional = false
 python-versions = ">=3.6"
 
-[[package]]
-name = "toml"
-version = "0.10.2"
-description = "Python Library for Tom's Obvious, Minimal Language"
-category = "dev"
-optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-
 [[package]]
 name = "tomli"
-version = "2.0.0"
+version = "2.0.1"
 description = "A lil' TOML parser"
 category = "dev"
 optional = false
@@ -654,15 +649,15 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "tomlkit"
-version = "0.7.0"
+version = "0.10.2"
 description = "Style preserving TOML library"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6,<4.0"
 
 [[package]]
 name = "tqdm"
-version = "4.62.3"
+version = "4.64.0"
 description = "Fast, Extensible Progress Meter"
 category = "dev"
 optional = false
@@ -674,6 +669,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 [package.extras]
 dev = ["py-make (>=0.1.0)", "twine", "wheel"]
 notebook = ["ipywidgets (>=6)"]
+slack = ["slack-sdk"]
 telegram = ["requests"]
 
 [[package]]
@@ -698,22 +694,22 @@ urllib3 = ">=1.26.0"
 
 [[package]]
 name = "typing-extensions"
-version = "4.0.1"
-description = "Backported and Experimental Type Hints for Python 3.6+"
+version = "4.2.0"
+description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "urllib3"
-version = "1.26.8"
+version = "1.26.9"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
 
 [package.extras]
-brotli = ["brotlipy (>=0.6.0)"]
+brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
 secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
@@ -727,457 +723,81 @@ python-versions = "*"
 
 [[package]]
 name = "zipp"
-version = "3.7.0"
+version = "3.8.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8,<3.10"
-content-hash = "c1b27cf9297e4777e78a72caba5f560be87a0f3b27c001b7a05b18adfdca2d1c"
+content-hash = "1e52cabf54af905e05d979683b28779e59690cf38ad4f805dbbf455b19d0a337"
 
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pyproject.toml

@@ -1,18 +1,20 @@
 [tool.poetry]
 name = "deepdog"
-version = "0.6.0"
+version = "0.6.4"
 description = ""
 authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"]
 
 [tool.poetry.dependencies]
 python = "^3.8,<3.10"
-pdme = "0.8.2"
+pdme = "^0.8.6"
+numpy = "1.22.3"
+scipy = "1.10.1"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=6"
 flake8 = "^4.0.1"
 pytest-cov = "^3.0.0"
-mypy = "^0.950"
+mypy = "^0.971"
 python-semantic-release = "^7.24.0"
 black = "^22.3.0"