Release 0.0.1

softboiler · Aug 11, 2023 · a173caa · a173caa
1 parent 00bad75
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diff --git a/.copier-answers.yml b/.copier-answers.yml
@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 47b9a0d
+_commit: 42d3de7
 _src_path: gh:blakeNaccarato/copier-python
 actions_runner: ubuntu-latest
 active: true
@@ -9,6 +9,6 @@ project_email: blake.naccarato@gmail.com
 project_name: boilerdata
 project_owner_github_username: blakeNaccarato
 project_owner_name: Blake Naccarato
-project_version: 0.0.0
+project_version: 0.0.1
 python_version: '3.11'
 year_of_project_creation: 2022
diff --git a/.env b/.env
@@ -1,17 +1,5 @@
 # Enable rich feedback and exceptions at the command line
-PYTHONSTARTUP = pythonrc.py
+PYTHONSTARTUP = .tools/scripts/pythonstartup.py
 PYDEVD_DISABLE_FILE_VALIDATION=1
-# default: Warn for all warnings, even `DeprecationWarning`
-# pkg_resources: https://github.com/blakeNaccarato/copier-python/issues/319#issue-1609228740
-# Creating a LegacyVersion: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1454209165
-# pre_commit read_text and open_text: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1455177114
-# imp module and ABCs: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1455183241
-# dpath...pkg_resources: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1457219723
-# unclosed file...plumbum: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1458742412
-# ignore:is still running:subprocess:ResourceWarning:subprocess: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1493072447
-# ignore:BuiltinImporter.module_repr:DeprecationWarning:importlib._bootstrap: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1493542865
-# ignore:lib2to3: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1502112446
-# ignore:ImportDenier:ImportWarning: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1546359005
-# ignore:numpy.ndarray size changed:RuntimeWarning: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1546360423
-# ignore::DeprecationWarning:sphinx.util.images...sphinx_book_theme: https://github.com/blakeNaccarato/copier-python/issues/319#issuecomment-1591786172
-PYTHONWARNINGS = default,ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning,ignore:Creating a LegacyVersion has been deprecated and will be removed in the next major release:DeprecationWarning:pip._vendor.packaging.version,ignore:read_text is deprecated:DeprecationWarning:pre_commit.util,ignore:open_text is deprecated:DeprecationWarning:importlib.resources._legacy,ignore:the imp module is deprecated in favour of importlib:DeprecationWarning:googlecloudsdk.core.util.importing,ignore:Using or importing the ABCs:DeprecationWarning:jsonschema.compat,ignore:The dpath.util package is being deprecated.:DeprecationWarning:dvc.dependency.param,ignore:unclosed file:ResourceWarning:dvc.stage.cache,ignore:the imp module is deprecated:DeprecationWarning:ansiwrap.core,ignore:unclosed file:ResourceWarning:ansiwrap.core,ignore:Jupyter is migrating its paths to use standard platformdirs:DeprecationWarning:jupyter_client.connect,ignore:the file is not specified with any extension:UserWarning:papermill.iorw,ignore:Passing unrecognized arguments to super:DeprecationWarning:traitlets.config.configurable,ignore:pkg_resources is deprecated as an API:DeprecationWarning,ignore:unclosed file:ResourceWarning:plumbum.commands.base,ignore:Passing unrecognized arguments to super:DeprecationWarning:ipywidgets.widgets.widget,ignore:`ipykernel.pylab.backend_inline` is deprecated:DeprecationWarning:ipykernel.pylab.backend_inline,ignore:subprocess:ResourceWarning:subprocess,ignore:BuiltinImporter.module_repr:DeprecationWarning:importlib._bootstrap,ignore:lib2to3 package is deprecated and may not be able to parse Python:PendingDeprecationWarning,ignore:lib2to3 package is deprecated and may not be able to parse Python:DeprecationWarning,ignore:ImportDenier:ImportWarning,ignore:numpy.ndarray size changed:RuntimeWarning,ignore::DeprecationWarning:sphinx.util.images,ignore::DeprecationWarning:myst_nb.sphinx_ext,ignore::DeprecationWarning:myst_parser.mdit_to_docutils.base,ignore::DeprecationWarning:optparse,ignore:Proactor event loop:RuntimeWarning:zmq._future,ignore::PendingDeprecationWarning:myst_nb.ext.execution_tables,ignore::PendingDeprecationWarning:sphinx_book_theme
+# ! Don't edit below. `warning_filters.py` may trash any changes.
+PYTHONWARNINGS=default,ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning,ignore:Creating a LegacyVersion has been deprecated and will be removed in the next major release:DeprecationWarning:pip._vendor.packaging.version,ignore:read_text is deprecated:DeprecationWarning:pre_commit.util,ignore:open_text is deprecated:DeprecationWarning:importlib.resources._legacy,ignore:the imp module is deprecated in favour of importlib:DeprecationWarning:googlecloudsdk.core.util.importing,ignore:Using or importing the ABCs:DeprecationWarning:jsonschema.compat,ignore:The dpath.util package is being deprecated.:DeprecationWarning:dvc.dependency.param,ignore:unclosed file:ResourceWarning:dvc.stage.cache,ignore:the imp module is deprecated:DeprecationWarning:ansiwrap.core,ignore:unclosed file:ResourceWarning:ansiwrap.core,ignore:Jupyter is migrating its paths to use standard platformdirs:DeprecationWarning:jupyter_client.connect,ignore:the file is not specified with any extension:UserWarning:papermill.iorw,ignore:Passing unrecognized arguments to super:DeprecationWarning:traitlets.config.configurable,ignore:pkg_resources is deprecated as an API:DeprecationWarning,ignore:unclosed file:ResourceWarning:plumbum.commands.base,ignore:Passing unrecognized arguments to super:DeprecationWarning:ipywidgets.widgets.widget,ignore:`ipykernel.pylab.backend_inline` is deprecated:DeprecationWarning:ipykernel.pylab.backend_inline,ignore:subprocess:ResourceWarning:subprocess,ignore:BuiltinImporter.module_repr:DeprecationWarning:importlib._bootstrap,ignore:lib2to3 package is deprecated and may not be able to parse Python:PendingDeprecationWarning,ignore:lib2to3 package is deprecated and may not be able to parse Python:DeprecationWarning,ignore:ImportDenier:ImportWarning,ignore:numpy.ndarray size changed:RuntimeWarning,ignore::DeprecationWarning:sphinx.util.images,ignore::DeprecationWarning:myst_nb.sphinx_ext,ignore::DeprecationWarning:myst_parser.mdit_to_docutils.base,ignore::DeprecationWarning:optparse,ignore:Proactor event loop:RuntimeWarning:zmq._future,ignore::PendingDeprecationWarning:myst_nb.ext.execution_tables,ignore::PendingDeprecationWarning:sphinx_book_theme,ignore:Please use `binary_dilation`:DeprecationWarning:trackpy.uncertainty,ignore:Importing clear_output from IPython.core.display is deprecated:DeprecationWarning:trackpy.utils,ignore:distutils Version classes are deprecated. Use packaging.version instead.:DeprecationWarning,ignore:unclosed file <_io.BufferedReader name:ResourceWarning,ignore:subpackages can technically be lazily loaded:RuntimeWarning
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -126,6 +126,7 @@ repos:
     rev: "23.7.0"
     hooks:
       - id: "black"
+      - id: "black-jupyter"
   - repo: "https://github.com/charliermarsh/ruff-pre-commit"
     rev: "v0.0.282"
     hooks:
@@ -166,7 +167,5 @@ repos:
   - repo: "https://github.com/nbQA-dev/nbQA"
     rev: "1.7.0"
     hooks:
-      - id: "nbqa-black"
-        additional_dependencies: ["black==23.7.0"]
       - id: "nbqa-ruff"
         additional_dependencies: ["ruff==0.0.282"]
diff --git a/.tools/requirements/requirements_both.txt b/.tools/requirements/requirements_both.txt
@@ -11,10 +11,9 @@ copier==8.1.0
 flit==3.9.0
 
 # Type checking
-pyright
+pyright==1.1.321
 
 # Pre-commit common requirements
-black==23.7.0
 ruff==0.0.282
 
 # Testing

diff --git a/.tools/requirements/requirements_dev.txt b/.tools/requirements/requirements_dev.txt
@@ -24,6 +24,7 @@ rich==13.5.2
 ipython==8.14.0
 
 # Format
+black[jupyter]==23.7.0
 sourcery-cli==1.6.0
 
 # Profiling

diff --git a/.vscode/tasks.json b/.vscode/tasks.json
@@ -39,16 +39,6 @@
   "tasks": [
     // * -------------------------------------------------------------------------- * //
     // * Changes below should persist in significant template updates.
-    {
-      "label": "dvc: repro force downstream",
-      "dependsOrder": "sequence",
-      "dependsOn": ["dvc: synchronize params"],
-      "type": "process",
-      "command": "pwsh",
-      "args": ["-Command", "dvc repro --force --downstream ${input:stage}"],
-      "icon": { "id": "graph" },
-      "problemMatcher": []
-    },
     {
       "label": "dvc: repro",
       "dependsOrder": "sequence",
@@ -60,39 +50,26 @@
       "problemMatcher": []
     },
     {
-      "label": "dvc: repro force all",
+      "label": "dvc: repro force downstream",
       "dependsOrder": "sequence",
-      "dependsOn": [
-        "setup: Update project",
-        "dvc: synchronize params",
-        "dvc: freeze",
-        "git: Stage all files",
-        "pre-commit",
-        "git: Stage all files"
-      ],
+      "dependsOn": ["dvc: synchronize params"],
       "type": "process",
       "command": "pwsh",
-      "args": ["-Command", "dvc repro --force"],
+      "args": ["-Command", "dvc repro --force-downstream ${input:stage}"],
       "icon": { "id": "graph" },
       "problemMatcher": []
     },
     {
-      "label": "dvc: repro all",
+      "label": "dvc: repro force",
       "dependsOrder": "sequence",
-      "dependsOn": [
-        "setup: Update project",
-        "dvc: synchronize params",
-        "dvc: freeze",
-        "git: Stage all files",
-        "pre-commit",
-        "git: Stage all files"
-      ],
+      "dependsOn": ["dvc: synchronize params"],
       "type": "process",
       "command": "pwsh",
-      "args": ["-Command", "dvc repro"],
+      "args": ["-Command", "dvc repro --force ${input:stage}"],
       "icon": { "id": "graph" },
       "problemMatcher": []
     },
+
     {
       "label": "dvc: dag",
       "dependsOrder": "sequence",
@@ -114,14 +91,6 @@
       "icon": { "id": "graph" },
       "problemMatcher": []
     },
-    {
-      "label": "dvc: freeze",
-      "type": "shell",
-      "options": { "shell": { "executable": "pwsh", "args": ["-Command"] } },
-      "command": "pip freeze --requirement .tools/requirements/requirements.txt --local --exclude-editable > repro.txt",
-      "icon": { "id": "graph" },
-      "problemMatcher": []
-    },
     // * -------------------------------------------------------------------------- * //
     // * WSL-SPECIFIC * //
     {

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,9 +9,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Nothing yet
 
+## [0.0.1]
+
+- Implement tests
+- Refactor out logic for models containing just file paths and project paths
+- Flatten the paths model parameters
+- Decouple latest development dependency versions from lower bounds in `pyproject.toml`
+
 ## [0.0.0]
 
 - Freeze requirements used for pipeline reproduction in `repro.txt` for this release
 
-[Unreleased]: https://github.com/blakeNaccarato/boilerdata/compare/0.0.0...HEAD
+[Unreleased]: https://github.com/blakeNaccarato/boilerdata/compare/0.0.1...HEAD
+[0.0.1]: https://github.com/blakeNaccarato/boilerdata/releases/tag/0.0.1
 [0.0.0]: https://github.com/blakeNaccarato/boilerdata/releases/tag/0.0.0
diff --git a/docs/conf.py b/docs/conf.py
@@ -2,13 +2,13 @@
 
 project = ""
 html_title = "boilerdata"
-copyright = f"{date.today().year}, Blake Naccarato, Kwang Jin Kim"  # noqa: A001
-version = "0.0.0"
+copyright = f"{date.today().year}, Blake Naccarato"  # noqa: A001
+version = "0.0.1"
 master_doc = "index"
 language = "en"
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 html_theme = "sphinx_book_theme"
-extensions = ["myst_parser", "sphinx_design", "sphinxcontrib.mermaid"]
+extensions = ["myst_parser", "sphinx_design"]
 # https://sphinx-book-theme.readthedocs.io/en/stable/reference.html#reference-of-theme-options
 html_theme_options = {
     "path_to_docs": "docs",

diff --git a/dvc.lock b/dvc.lock
@@ -51,8 +51,8 @@ stages:
     outs:
     - path: data/modelfun
       hash: md5
-      md5: fe0656588888ce19d4b3cabeeb66aa27.dir
-      size: 60136
+      md5: 0bca910877e3b8387ba1311ada4832c2.dir
+      size: 60067
       nfiles: 1
   runs:
     cmd: python -m boilerdata.stages.runs
@@ -90,8 +90,8 @@ stages:
       nfiles: 1
     - path: data/modelfun
       hash: md5
-      md5: fe0656588888ce19d4b3cabeeb66aa27.dir
-      size: 60136
+      md5: 0bca910877e3b8387ba1311ada4832c2.dir
+      size: 60067
       nfiles: 1
     - path: data/runs
       hash: md5
@@ -100,8 +100,8 @@ stages:
       nfiles: 1
     - path: src/boilerdata/stages/pipeline.py
       hash: md5
-      md5: 940d214f9890f82709e907b47aa6c98a
-      size: 8938
+      md5: 71728116e120fb597e375e12e256f717
+      size: 8905
     - path: src/boilerdata/validation.py
       hash: md5
       md5: 3bf12c7498eae3ab299f2776be0ce064
@@ -134,52 +134,52 @@ stages:
     outs:
     - path: data/results
       hash: md5
-      md5: d46e3b9c9a88cd4d01a464cc03ddd912.dir
-      size: 235130
+      md5: 8645a483c5bb8611bf3b865b487f96d5.dir
+      size: 235134
       nfiles: 1
   metrics:
     cmd: ploomber-engine src/boilerdata/stages/metrics.ipynb NUL
     deps:
     - path: data/results
       hash: md5
-      md5: d46e3b9c9a88cd4d01a464cc03ddd912.dir
-      size: 235130
+      md5: 8645a483c5bb8611bf3b865b487f96d5.dir
+      size: 235134
       nfiles: 1
     - path: src/boilerdata/stages/metrics.ipynb
       hash: md5
-      md5: 6ebf997408248cb991c008ec61424193
-      size: 7556
+      md5: cdfac0be8e69ebd6b3f3373bac728212
+      size: 7504
     params:
       params.yaml:
         do_plot: true
     outs:
     - path: data/metrics/plots/error_T_s.png
       hash: md5
-      md5: 770a235b7ffca10bc71d8fc5e5cfa7ca
-      size: 125605
+      md5: a8c6ac008f83de621cdca414ff6f03f1
+      size: 124366
     - path: data/metrics/plots/error_h_a.png
       hash: md5
-      md5: ae889a01f63fb2f2fcb47f7245607315
-      size: 206579
+      md5: 8835ee8054fd5ade3c53a80ca08a8bcd
+      size: 210439
     - path: data/metrics/plots/error_q_s.png
       hash: md5
-      md5: 68bc0e1b108f183129bbedb0cb416d69
-      size: 175942
+      md5: d875825eb2b305bbb50a42a45b9ea0a4
+      size: 179555
     - path: data/metrics/plots/new_fit_0.png
       hash: md5
       md5: 5e6067f396efc35e7fd7ca22b484f108
       size: 119322
     - path: data/metrics/plots/new_fit_1.png
       hash: md5
-      md5: e9698e1483bc90f56ed69fc4b5498fc0
-      size: 113970
+      md5: f1b24f6e955d6281d77e5b08186bf8b5
+      size: 113613
     - path: data/metrics/plots/new_fit_2.png
       hash: md5
-      md5: af49877b1a50b9b89c7e73fcada72684
-      size: 125344
+      md5: a0aba8c7a4737288d0c96463c149390a
+      size: 145431
     - path: data/metrics/tables/pipeline_metrics.json
       hash: md5
-      md5: 1aa224e207ef9602b1fa51fe360d52c2
+      md5: 78255ff52f10a50b73b656ce80f57305
       size: 207
   literature:
     cmd: python -m boilerdata.stages.literature
@@ -191,13 +191,13 @@ stages:
       nfiles: 9
     - path: src/boilerdata/models
       hash: md5
-      md5: 83b50eb5fbb0d13e1346788de460fd62.dir
-      size: 31189
+      md5: cceed6391a3abc02e8ce0952565ec8a3.dir
+      size: 31190
       nfiles: 7
     - path: src/boilerdata/stages/literature.py
       hash: md5
-      md5: 827c5400c0cf0482df4ac5997864f454
-      size: 3313
+      md5: 4ccb001a11f740873988f6333f90976d
+      size: 3322
     outs:
     - path: data/literature_results
       hash: md5
@@ -209,21 +209,17 @@ stages:
     deps:
     - path: .tools/requirements
       hash: md5
-      md5: 837cdbaa59c3b9a5b1e17a8d34a0ed16.dir
-      size: 1893
-      nfiles: 4
+      md5: 71b80ef4e21a86f12ab66ab0003930ea.dir
+      size: 2459
+      nfiles: 6
     - path: config/axes.yaml
       hash: md5
       md5: 5f95c2418c2d82618d10d711a50c0f2f
       size: 2320
-    - path: requirements.txt
-      hash: md5
-      md5: c3d5e7eee07c3c2eced5512b0a4bf7fa
-      size: 563
     - path: src/boilerdata/models
       hash: md5
-      md5: 83b50eb5fbb0d13e1346788de460fd62.dir
-      size: 31189
+      md5: cceed6391a3abc02e8ce0952565ec8a3.dir
+      size: 31190
       nfiles: 7
     - path: src/boilerdata/stages/axes.py
       hash: md5

diff --git a/dvc_repro.ps1 b/dvc_repro.ps1
diff --git a/frozen_requirements.txt b/frozen_requirements.txt
diff --git a/pyproject.toml b/pyproject.toml
@@ -10,7 +10,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "boilerdata"
-version = "0.0.0"
+version = "0.0.1"
 description = "Data processing pipeline for a nucleate pool boiling apparatus."
 readme = "README.md"
 license = { file = "LICENSE" }
@@ -23,7 +23,7 @@ dependencies = [
     "matplotlib>=3.7.2",
     "nbqa>=1.7.0",
     "pandas[hdf5,performance]>=2.0.2",
-    "pandas-stubs~=2.0.2",
+    "pandas-stubs>=2.0.2",
     "pandera>=0.16.1",
     "ploomber-engine>=0.0.30",
     "propshop>=0.1.1",
@@ -64,6 +64,7 @@ ignore_undeclared = [
     "graphviz",  # .tools/requirements/requirements_docs.txt
     "originpro", # .tools/requirements/requirements_dev.txt
     "pytest",
+    "rich",      # .tools/requirements/requirements_dev.txt
 ]
 
 [tool.ruff]

diff --git a/tests/data/data/modelfun/model.dillpickle b/tests/data/data/modelfun/model.dillpickle