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Fix install #26

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merged 6 commits into from
Sep 27, 2024
Merged

Fix install #26

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baaa002
fixed casing
haeussma Sep 27, 2024
b4aaaa6
Refactor package name in pyproject.toml
haeussma Sep 27, 2024
f27d1aa
Refactor pyenzyme.py and SAHH_kinetics.ipynb
haeussma Sep 27, 2024
feefe82
updated pyproject.toml
haeussma Sep 27, 2024
abd4768
Refactor pyproject.toml and fix casing
haeussma Sep 27, 2024
f07fe61
rerun tests
haeussma Sep 27, 2024
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39 changes: 7 additions & 32 deletions docs/examples/SAHH_kinetics.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -144578,13 +144578,13 @@
{
"data": {
"text/html": [
"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">📍 Assigned <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">228</span> initial concentration coditions for <span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">[</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TmSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SIH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'McSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'BUFFER'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MhSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SAH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'Hyc'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span>\n",
"<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MtSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'DTNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">]</span> from data/plate_map_SAHH_kinetics.xlsx to the plate.\n",
"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">📍 Assigned <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">228</span> initial concentration coditions for <span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">[</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MhSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MtSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'McSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SAH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'DTNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'Hyc'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'BUFFER'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span>\n",
"<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SIH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TmSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">]</span> from data/plate_map_SAHH_kinetics.xlsx to the plate.\n",
"</pre>\n"
],
"text/plain": [
"📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\n",
"\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n"
"📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\n",
"\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n"
]
},
"metadata": {},
Expand Down Expand Up @@ -144837,7 +144837,9 @@
"plate.blank_species(BUFFER)\n",
"\n",
"# Then the all other species\n",
"plate.blank_species(SAH)\n",
"plate.blank_species(\n",
" SAH,\n",
")\n",
"plate.blank_species(SIH)\n",
"plate.blank_species(McSAHH)\n",
"plate.blank_species(MtSAHH)\n",
Expand Down Expand Up @@ -147708,33 +147710,6 @@
"name": "stdout",
"output_type": "stream",
"text": [
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"✅ Added measurements from 6 wells with concentration values to EnzymeMLDocument\n"
]
}
Expand Down
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