added project.toml file and removed setup.py

mpecchi · Mar 9, 2024 · 3489336 · 3489336
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diff --git a/docs/index.rst b/docs/index.rst
@@ -20,7 +20,7 @@ Welcome to gcms_data_analysis's documentation!
    :caption: Contents:
 
 
-   source/modules
+   source/gcms_data_analysis
 
 Indices and tables
 ==================

diff --git a/e b/e
@@ -0,0 +1,317 @@
+[33mcommit c5fdeb55be031f4789f01054639fc7f47e286d32[m[33m ([m[1;36mHEAD -> [m[1;32mmain[m[33m, [m[1;31morigin/main[m[33m)[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 28 18:10:01 2024 -0600
+
+    added samples_info_std to create_samples_info
+
+[33mcommit 944ab713df28272b594615964aa8590de3c98478[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 28 12:16:54 2024 -0600
+
+    minor mods
+
+[33mcommit 18f4bcc200adee55c2c5c926fb8ec7cda9d8cbd9[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 28 11:58:51 2024 -0600
+
+    extracted imports from Fragmenter class
+
+[33mcommit 75b53fea460e30f971c14aed77c49c405dcb018b[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 28 11:15:53 2024 -0600
+
+    added project_urls to docum in setup.py
+
+[33mcommit 1ad5641ee6c98ef7a8e17641d5b41809a45b2abd[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 20:24:57 2024 -0600
+
+    test for docs
+
+[33mcommit a0b7d8016e6dff03c2d65041a21bf1f8a6fa8b20[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 20:24:00 2024 -0600
+
+    documentation tests
+
+[33mcommit 31b460165e6ba159ef3ae521316060546b087a9b[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 20:15:32 2024 -0600
+
+    maybe badge for coverage
+
+[33mcommit 40c18dd33922c4c7628b4d7de53603bc0170c9f7[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 19:55:09 2024 -0600
+
+    added --cov-report=term to pytest.ini
+
+[33mcommit 4c78b738c0cde11c8fcb90c96afae4d6421a1e5b[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 19:48:29 2024 -0600
+
+    fix gha
+
+[33mcommit 7705df88ef0fba164e06e77999707e4ccc5801db[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 19:44:47 2024 -0600
+
+    github action fix
+
+[33mcommit f4d8910ae7df5b3f34bb4a0e9b804727d41e75e0[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 19:32:10 2024 -0600
+
+    added link to readthedocs and hopefully fixed gha
+
+[33mcommit 1ae388673991d7dd96803ae634f23806c943bc08[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 19:29:22 2024 -0600
+
+    xml to term
+
+[33mcommit 53b01867244e0824793ff90c78c4de2efd765bf8[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 19:25:55 2024 -0600
+
+    updated workflow actions
+
+[33mcommit a076696ecb09bedc24b67874be64be03ccc3340b[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 19:22:42 2024 -0600
+
+    added test badge
+
+[33mcommit 944fc720f04decb57c70c3d5e4e5713e6d789e25[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 19:15:20 2024 -0600
+
+    fixed conftest
+
+[33mcommit c7fa8afd25a5126466fc0162595288108a5319ad[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 18:31:37 2024 -0600
+
+    fixed sorted in create_files_info
+
+[33mcommit 8d6a6507d08456e796bcb97c09b19043ec0ae7d9[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 18:23:39 2024 -0600
+
+    fixed sorted issues in tests
+
+[33mcommit 68127317d5f9a30cecc929976608d68e4a31ae99[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 18:13:37 2024 -0600
+
+    githubactions 2
+
+[33mcommit ac8856dc0cd1ab3e271eee795fda9d6ab544749b[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 18:11:32 2024 -0600
+
+    test1 of github actions for tests
+
+[33mcommit 9671a4ff5edf84f08485890ce777ce8f1f607a7c[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 17:50:57 2024 -0600
+
+    updated docs
+
+[33mcommit 8743c00269707932cdafeeb1512519cd9266f94b[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 15:18:39 2024 -0600
+
+    RCS data and code update
+
+[33mcommit b1124e1d0236cab3923048f89ec56c081d0ace35[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 14:12:50 2024 -0600
+
+    added data for RCS revisions
+
+[33mcommit 1af47e4648fe3801629909dd9609d48c11d457fc[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 14:12:17 2024 -0600
+
+    added data for RCS revisions
+
+[33mcommit 85d32e029906ae3c1206eb8d048d79c929b23d01[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 27 11:32:49 2024 -0600
+
+    fixed hetero atoms in compounds properties
+
+[33mcommit a9097a105ce82ccc65dedeb24d107ddd25da84eb[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 21 15:15:46 2024 -0500
+
+    requirements added
+
+[33mcommit a419b6a092b5a8552d9b9af754181e7e9f7e7534[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 21 15:14:39 2024 -0500
+
+    docs
+
+[33mcommit 905df4486e439581a9086bd5b55f6714d4577e3c[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 21 13:48:49 2024 -0500
+
+    docs
+
+[33mcommit 59d4d1d10d1a7d2905d148d5ce3cb1c453908792[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 21 13:37:36 2024 -0500
+
+    docs
+
+[33mcommit 59f441cb084605d4287185ecd6d83356f4655737[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 21 12:33:57 2024 -0500
+
+    requirements updated
+
+[33mcommit 43c3c382b8dd042f52746a2e9ff3e7e0d85f820b[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 21 12:30:55 2024 -0500
+
+    updated requirements
+
+[33mcommit 99e971351c8071329c8243bc83c63374b5af7835[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 21 12:28:59 2024 -0500
+
+    added docs/requirements.txt
+
+[33mcommit 09157273931126ed081f485f8f6e13e3d6a2c132[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 21 12:28:46 2024 -0500
+
+    updated readthedocs
+
+[33mcommit a9e47b2bafe80d1f4aa4b8b5a000bd689bb1f343[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 21 09:33:27 2024 -0500
+
+    doc built with sphinx, trying to host it at rtd
+
+[33mcommit 84c7e871bacbec6fb30949c46def340abf4a0ba0[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 20 18:09:50 2024 -0500
+
+    updated paper.md, 1st internal revisions
+
+[33mcommit f385cad65df31df7224607a0bd851c8e06acae25[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 20 17:29:22 2024 -0500
+
+    added paper.md for submission to JOSS
+
+[33mcommit d30425fc4240d259133e50373a9ada537c34bb6e[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Tue Feb 20 10:45:26 2024 -0500
+
+    fully tested v1.0.1
+
+[33mcommit d0d5c9d74859fa392f9570d04d25e6ee6425a82d[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Mon Feb 19 21:24:41 2024 -0500
+
+    tests added, v=1.0.0
+
+[33mcommit dd53928b9c8f278ad1438e2a5d422cc5dae4a7f4[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Fri Feb 16 18:40:50 2024 -0500
+
+    version change
+
+[33mcommit 5b76b22e8e2247f85c68f21f7a203c6116cad957[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Fri Feb 16 18:40:13 2024 -0500
+
+    minor changes
+
+[33mcommit 55f45f12fe66a875c3fecef091941e8b29b8a7a5[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Thu Feb 15 10:06:51 2024 -0500
+
+    readme updated
+
+[33mcommit 04f03f042cbe2945ee9fcee7d445ce337f42f8ec[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Mon Feb 12 10:00:08 2024 -0500
+
+    updated documentation and readme (automatically)
+
+[33mcommit 4481c5a64221f47e5abb1a4b38c94cb80698f7bd[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Sun Feb 11 17:21:29 2024 -0500
+
+    updated documentation to each method
+
+[33mcommit 9297cc04f875902a10c4ddc9a17d18d89455f706[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Fri Feb 9 16:18:30 2024 -0500
+
+    fixed labels for plots with conc_if_undiluted
+
+[33mcommit a7a58717541585932c76920035146a6856f21261[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Fri Feb 9 09:30:07 2024 -0500
+
+    added concentration if undiluted in files and samples
+
+[33mcommit 2c1b07a35e227f67ec28d4b3bd53cf7fc33cb5b6[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Thu Feb 8 11:19:54 2024 -0500
+
+    fixed files_param
+
+[33mcommit 39873d96b15f44f152de40850929be4fd4bc71c7[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Thu Feb 8 10:41:00 2024 -0500
+
+    added files and samples report creation
+
+[33mcommit f62ffe7c84d5e83bfb032f68e2614f810cf9ceab[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 7 16:22:16 2024 -0500
+
+    minor
+
+[33mcommit aabf7374133fd8b7732dba08cfda3c2d3e719d00[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 7 16:11:58 2024 -0500
+
+    minor
+
+[33mcommit 14810a2c00ef7c06dc14ce1b16c5dd1e8c6b8ab1[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 7 16:11:29 2024 -0500
+
+    minor
+
+[33mcommit 96137435ad7e66c96569642fba8559874beb5761[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 7 16:10:52 2024 -0500
+
+    minor
+
+[33mcommit 5fdd5bf356987296f49ba087178751ab68ac045b[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 7 16:09:50 2024 -0500
+
+    updated gitignore
+
+[33mcommit a85cf64729185b3242bef5e13c9958e47faab30b[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 7 16:07:28 2024 -0500
+
+    fixed example and removed output from tracking
+
+[33mcommit 7ec492935bada67e696a11c7b5bd3a7692526512[m
+Author: mpecchi <matteo.pecchi@gmail.com>
+Date:   Wed Feb 7 15:55:18 2024 -0500
+
+    first init of the repo with fully working package
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,37 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "gcms_data_analysis"
+version = "1.0.3"
+authors = [{ name = "Matteo Pecchi" }]
+description = "Automatic analysis of GC-MS data"
+readme = "README.md"
+license = { file = "LICENSE" }  # Ensure the file name matches the case (e.g., LICENSE or license)
+
+# Dependencies directly under [project]
+dependencies = [
+    "numpy",
+    "pandas",
+    "matplotlib",
+    "seaborn",
+    "ele",
+    "pubchempy",
+    "rdkit",
+    "openpyxl",
+    "pyarrow"
+]
+
+# Classifiers directly under [project]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+requires-python = ">=3.6"
+
+[project.urls]
+Homepage = "https://github.com/mpecchi/gcms_data_analysis/tree/main"
+Documentation = "https://gcms-data-analysis.readthedocs.io/en/latest/"
diff --git a/setup.py b/setup.py
diff --git a/gcms_data_analysis/__init__.py → src/gcms_data_analysis/__init__.py b/gcms_data_analysis/__init__.py → src/gcms_data_analysis/__init__.py
diff --git a/gcms_data_analysis/main.py → src/gcms_data_analysis/main.py b/gcms_data_analysis/main.py → src/gcms_data_analysis/main.py