From 56de5b801879cbf140eccf4f7b42a2c72af7556f Mon Sep 17 00:00:00 2001
From: Frank Bergmann <frank.thomas.bergmann@gmail.com>
Date: Thu, 26 Sep 2024 18:35:12 +0200
Subject: [PATCH 1/3]  - correct casing (#23)

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index e822e1a..138f14f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,8 +5,8 @@ description = "Tool to work with microtiter plate data."
 authors = ["haeussma <83341109+haeussma@users.noreply.github.com>"]
 license = "MIT License"
 readme = "README.md"
-packages = [{ include = "mtphandler" }]
-include = ["mtphandler/units/ontomaps.toml"]
+packages = [{ include = "MTPHandler" }]
+include = ["MTPHandler/units/ontomaps.toml"]
 
 
 [tool.poetry.dependencies]

From 257a0df0a389e22337c2488baef5b3c9ba732a0e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Max=20H=C3=A4u=C3=9Fler?=
 <max.haeussler@ibtb.uni-stuttgart.de>
Date: Fri, 27 Sep 2024 18:18:58 +0200
Subject: [PATCH 2/3] fixed casing (#25)

* fixed casing in `pyproject.toml`
---
 docs/examples/SAHH_kinetics.ipynb           |  73 ++---
 docs/examples/data/enzymeml_TmSAHH_SAH.json | 324 ++++++++++----------
 mtphandler/ioutils/pyenzyme.py              |   1 -
 3 files changed, 193 insertions(+), 205 deletions(-)

diff --git a/docs/examples/SAHH_kinetics.ipynb b/docs/examples/SAHH_kinetics.ipynb
index 7f553a2..ac55366 100644
--- a/docs/examples/SAHH_kinetics.ipynb
+++ b/docs/examples/SAHH_kinetics.ipynb
@@ -92,6 +92,20 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mtphandler.molecule import Protein\n",
+    "\n",
+    "my_variant = Protein(\n",
+    "    id=\"L191G\",\n",
+    "    name=\"L191G\",\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -144486,7 +144500,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144528,7 +144542,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144572,19 +144586,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "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\">'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\">'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\">'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\">'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\">'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\">'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\">'McSAHH'</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\">'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\">'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>\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'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\n",
+       "\u001b[1;35m'TmSAHH'\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"
       ]
      },
      "metadata": {},
@@ -144620,7 +144634,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -144837,7 +144851,9 @@
     "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",
@@ -144858,7 +144874,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -144898,7 +144914,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -147666,7 +147682,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -147701,40 +147717,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
      "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"
      ]
     }
@@ -147759,7 +147748,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -147818,7 +147807,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/docs/examples/data/enzymeml_TmSAHH_SAH.json b/docs/examples/data/enzymeml_TmSAHH_SAH.json
index 86e89e2..6b48bbd 100644
--- a/docs/examples/data/enzymeml_TmSAHH_SAH.json
+++ b/docs/examples/data/enzymeml_TmSAHH_SAH.json
@@ -18,7 +18,7 @@
                         "exponent": 1,
                         "multiplier": null,
                         "scale": 1.0,
-                        "ld_id": "enzml:BaseUnit/e3a5826c-6a95-4a55-8d70-7de603caeeef",
+                        "ld_id": "enzml:BaseUnit/7507fc3b-6f31-4ce7-99e4-3df87993a41c",
                         "ld_type": [
                             "enzml:BaseUnit"
                         ],
@@ -29,7 +29,7 @@
                         }
                     }
                 ],
-                "ld_id": "enzml:UnitDefinition/030e3102-7730-43e2-9ed9-098399412c85",
+                "ld_id": "enzml:UnitDefinition/2d99c27f-949b-40f8-acb9-02e22fd46fc5",
                 "ld_type": [
                     "OBO:UO_0000000"
                 ],
@@ -40,7 +40,7 @@
                 }
             },
             "constant": true,
-            "ld_id": "enzml:Vessel/76a8dec5-3654-4573-8098-9ea3331235ba",
+            "ld_id": "enzml:Vessel/2c2bacab-9361-4a5a-bfc9-25ef526dc2f0",
             "ld_type": [
                 "enzml:Vessel",
                 "OBO:OBI_0400081"
@@ -69,7 +69,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/dff2284a-054b-4e66-96ba-f92ee185a7bb",
+            "ld_id": "enzml:Protein/4e6f2068-6568-4dc8-8bad-5ca5b43ac58b",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -107,7 +107,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/4961f179-e073-41ca-bce4-0286377a06d8",
+            "ld_id": "enzml:Protein/7acc8306-c72d-46ef-b880-ab42b59c4d76",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -145,7 +145,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/2179befa-30d1-4f17-884e-a057038b06c4",
+            "ld_id": "enzml:Protein/fedc65c2-97f9-40e1-b78a-deef15e47ae8",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -183,7 +183,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/eb200fcd-3007-4fb7-a7cc-a5f06e77dd6f",
+            "ld_id": "enzml:Protein/a407c986-a00e-4921-921b-2fc5b25c8314",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -223,7 +223,7 @@
             "inchi": null,
             "inchikey": null,
             "references": [],
-            "ld_id": "enzml:SmallMolecule/f481edf4-a76a-48b1-84f8-640cb112c2b3",
+            "ld_id": "enzml:SmallMolecule/014feb9b-1b64-4208-9c73-9bf56f5d1c79",
             "ld_type": [
                 "enzml:SmallMolecule"
             ],
@@ -425,7 +425,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/b02ad738-ba90-4fad-be33-88df3b4d6217",
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -438,7 +438,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/5e3848e3-b8bf-4ef6-88d2-04775d342dd6",
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -468,7 +468,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8",
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -486,7 +486,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/e89451cc-ed51-4555-9e95-009af83fab5a",
+                    "ld_id": "enzml:MeasurementData/59b2d1e3-d027-4223-b313-c41894965c27",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -511,7 +511,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/b02ad738-ba90-4fad-be33-88df3b4d6217",
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -524,7 +524,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/5e3848e3-b8bf-4ef6-88d2-04775d342dd6",
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -1998,7 +1998,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8",
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -2016,7 +2016,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/be2bcbd4-123a-4570-9c26-7bf5ad6f65ad",
+                    "ld_id": "enzml:MeasurementData/b05df68c-0307-4346-b569-2addc828d601",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -2041,7 +2041,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/b02ad738-ba90-4fad-be33-88df3b4d6217",
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -2054,7 +2054,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/5e3848e3-b8bf-4ef6-88d2-04775d342dd6",
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -2084,7 +2084,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8",
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -2102,7 +2102,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/5e1dc785-a1df-48bb-91de-ecb3add28e79",
+                    "ld_id": "enzml:MeasurementData/af80fcc0-7300-46e6-bf76-b41a8cf3da5e",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -2128,7 +2128,7 @@
                         "exponent": 1,
                         "multiplier": null,
                         "scale": 1.0,
-                        "ld_id": "md:BaseUnit/b85e7df2-91c7-4053-8f1e-7ca0084e8f3b",
+                        "ld_id": "md:BaseUnit/d6cfa323-be66-4591-84d9-570e831169f8",
                         "ld_type": [
                             "md:BaseUnit"
                         ],
@@ -2137,7 +2137,7 @@
                         }
                     }
                 ],
-                "ld_id": "md:UnitDefinition/fe60fc54-3434-45e8-9f6c-209a362451b7",
+                "ld_id": "md:UnitDefinition/31f16537-09de-4045-ae55-ad3197ffcb70",
                 "ld_type": [
                     "OBO:UO_0000000"
                 ],
@@ -2145,7 +2145,7 @@
                     "md": "https://github.com/FAIRChemistry/MTPHandler"
                 }
             },
-            "ld_id": "enzml:Measurement/0e4bbe09-b53f-4112-95d9-505ecc85264a",
+            "ld_id": "enzml:Measurement/b4be0d27-2224-4ca7-9755-95d9d5616271",
             "ld_type": [
                 "enzml:Measurement"
             ],
@@ -2167,8 +2167,8 @@
             "name": "photometric measurement",
             "species_data": [
                 {
-                    "species_id": "DTNB",
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@@ -2178,7 +2178,7 @@
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@@ -2191,7 +2191,7 @@
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@@ -2209,7 +2209,7 @@
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@@ -2221,7 +2221,7 @@
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@@ -2239,7 +2239,7 @@
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@@ -2264,7 +2264,7 @@
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@@ -2277,7 +2277,7 @@
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@@ -2307,7 +2307,7 @@
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@@ -2325,7 +2325,7 @@
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@@ -2350,7 +2350,7 @@
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@@ -2363,7 +2363,7 @@
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@@ -3837,7 +3837,7 @@
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@@ -3855,7 +3855,7 @@
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@@ -3869,8 +3869,8 @@
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@@ -3880,7 +3880,7 @@
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@@ -3893,7 +3893,7 @@
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@@ -3911,7 +3911,7 @@
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@@ -3923,7 +3923,7 @@
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@@ -3941,7 +3941,7 @@
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@@ -3966,7 +3966,7 @@
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@@ -3979,7 +3979,7 @@
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@@ -4009,7 +4009,7 @@
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@@ -4041,8 +4041,8 @@
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@@ -4052,7 +4052,7 @@
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@@ -4065,7 +4065,7 @@
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@@ -4083,7 +4083,7 @@
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@@ -4095,7 +4095,7 @@
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@@ -4113,7 +4113,7 @@
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@@ -4139,7 +4139,7 @@
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@@ -4148,7 +4148,7 @@
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@@ -4156,7 +4156,7 @@
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@@ -4189,7 +4189,7 @@
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@@ -4202,7 +4202,7 @@
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@@ -4232,7 +4232,7 @@
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@@ -4275,7 +4275,7 @@
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@@ -4288,7 +4288,7 @@
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@@ -5762,7 +5762,7 @@
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@@ -5805,7 +5805,7 @@
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@@ -5818,7 +5818,7 @@
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@@ -5848,7 +5848,7 @@
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@@ -5866,7 +5866,7 @@
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@@ -5892,7 +5892,7 @@
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@@ -5901,7 +5901,7 @@
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@@ -5909,7 +5909,7 @@
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@@ -5931,8 +5931,8 @@
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@@ -5942,7 +5942,7 @@
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@@ -5955,7 +5955,7 @@
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@@ -5973,7 +5973,7 @@
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@@ -5985,7 +5985,7 @@
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@@ -9673,7 +9673,7 @@
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                     "time": [],
                     "time_unit": {
@@ -11451,7 +11451,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8",
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11469,7 +11469,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/bb5d1657-5ae7-4a95-ac06-8b4ccc425e3d",
+                    "ld_id": "enzml:MeasurementData/77bb27c6-8023-4f8b-843f-ded739c6dd73",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -11494,7 +11494,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/b02ad738-ba90-4fad-be33-88df3b4d6217",
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11507,7 +11507,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/5e3848e3-b8bf-4ef6-88d2-04775d342dd6",
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11537,7 +11537,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8",
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11555,7 +11555,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/b4aa2989-d17f-42cc-978e-2a2b9b108f69",
+                    "ld_id": "enzml:MeasurementData/b8ade515-0564-4685-917b-ef79f09213c6",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -11569,8 +11569,8 @@
                     }
                 },
                 {
-                    "species_id": "SAH",
-                    "initial": 200.0,
+                    "species_id": "DTNB",
+                    "initial": 500.0,
                     "data_unit": {
                         "id": null,
                         "name": "umol / l",
@@ -11580,7 +11580,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/b02ad738-ba90-4fad-be33-88df3b4d6217",
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11593,7 +11593,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/5e3848e3-b8bf-4ef6-88d2-04775d342dd6",
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11611,7 +11611,7 @@
                         }
                     },
                     "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
-                    "prepared": 200.0,
+                    "prepared": 500.0,
                     "data": [],
                     "time": [],
                     "time_unit": {
@@ -11623,7 +11623,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8",
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11641,7 +11641,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/83887dfb-858a-4173-a81b-70f19b5dc597",
+                    "ld_id": "enzml:MeasurementData/7a3c944e-98a4-4081-8158-c568833e4c1c",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -11667,7 +11667,7 @@
                         "exponent": 1,
                         "multiplier": null,
                         "scale": 1.0,
-                        "ld_id": "md:BaseUnit/b85e7df2-91c7-4053-8f1e-7ca0084e8f3b",
+                        "ld_id": "md:BaseUnit/d6cfa323-be66-4591-84d9-570e831169f8",
                         "ld_type": [
                             "md:BaseUnit"
                         ],
@@ -11676,7 +11676,7 @@
                         }
                     }
                 ],
-                "ld_id": "md:UnitDefinition/fe60fc54-3434-45e8-9f6c-209a362451b7",
+                "ld_id": "md:UnitDefinition/31f16537-09de-4045-ae55-ad3197ffcb70",
                 "ld_type": [
                     "OBO:UO_0000000"
                 ],
@@ -11684,7 +11684,7 @@
                     "md": "https://github.com/FAIRChemistry/MTPHandler"
                 }
             },
-            "ld_id": "enzml:Measurement/c7afd438-d8db-4b0a-9d3a-a90f06961ebf",
+            "ld_id": "enzml:Measurement/a1394bfd-038b-413d-aafb-2c28f8a3f465",
             "ld_type": [
                 "enzml:Measurement"
             ],
@@ -11704,7 +11704,7 @@
     ],
     "equations": [],
     "parameters": [],
-    "ld_id": "enzml:EnzymeMLDocument/fd4c9792-95e8-40e5-a4ef-cd0f2cdb3a93",
+    "ld_id": "enzml:EnzymeMLDocument/01d7bf76-39ee-42af-987b-2a1b46c13e6a",
     "ld_type": [
         "enzml:EnzymeMLDocument"
     ],
diff --git a/mtphandler/ioutils/pyenzyme.py b/mtphandler/ioutils/pyenzyme.py
index 3de83ca..6c37522 100644
--- a/mtphandler/ioutils/pyenzyme.py
+++ b/mtphandler/ioutils/pyenzyme.py
@@ -367,7 +367,6 @@ def add_to_species_data(
                 time_unit=EnzML_UnitDef(**time_unit.model_dump()),
                 data_type=DataTypes.CONCENTRATION,
             )
-            print(f"added temp unit {time_unit.name}")
 
     @staticmethod
     def map_protein(protein: Protein, vessel_id: str) -> pe.Protein:

From 4d804faca32716caaa8bcfdc563e62e343642760 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Max=20H=C3=A4u=C3=9Fler?=
 <max.haeussler@ibtb.uni-stuttgart.de>
Date: Fri, 27 Sep 2024 19:22:44 +0200
Subject: [PATCH 3/3] Update pyproject.toml

---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index badf906..7805e01 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,8 +5,8 @@ description = "Python package for processing, enriching, and converting microtit
 authors = ["haeussma <83341109+haeussma@users.noreply.github.com>"]
 license = "MIT License"
 readme = "README.md"
-packages = [{ include = "MTPHandler" }]
-include = ["MTPHandler/units/ontomaps.toml"]
+packages = [{ include = "mtphandler" }]
+include = ["mtphandler/units/ontomaps.toml"]
 
 
 [tool.poetry.dependencies]
@@ -38,4 +38,4 @@ requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.mypy]
-ignore_missing_imports = true
\ No newline at end of file
+ignore_missing_imports = true