Documentation update (#160)

* Changed README.md * Changed docs notebooks --------- Co-authored-by: Inga Ulusoy <inga.ulusoy@uni-heidelberg.de>
ssciwr · Oct 30, 2023 · fe1e937 · fe1e937
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diff --git a/README.md b/README.md
@@ -38,9 +38,11 @@ The `AMMICO` package can be installed using pip:
 ```
 pip install ammico
 ```
-This will install the package and its dependencies locally.
+This will install the package and its dependencies locally. If after installation you get some errors when running some modules, please follow the instructions below. 
 
-Some ammico components require tensorflow (e.g. Emotion detector), some pytorch (e.g. Summary detector). Sometimes there are compatibility problems between these two frameworks. To avoid compatibility problems on your machines, we suggest you to follow these steps before installing the package (you need conda on your machine):
+## Compatibility problems solving
+
+Some ammico components require `tensorflow` (e.g. Emotion detector), some `pytorch` (e.g. Summary detector). Sometimes there are compatibility problems between these two frameworks. To avoid these problems on your machines, you can prepare proper environment before installing the package (you need conda on your machine):
 
 ### 1. First, install tensorflow (https://www.tensorflow.org/install/pip)
 - create a new environment with python and activate it
@@ -68,7 +70,7 @@ Some ammico components require tensorflow (e.g. Emotion detector), some pytorch
 
     ```conda activate ammico_env ```
 
-- and now we can install tensorflow
+- install tensorflow
 
     ```python -m pip install tensorflow==2.12.1```
 
@@ -85,7 +87,7 @@ Some ammico components require tensorflow (e.g. Emotion detector), some pytorch
 It is done.
     
 ### Micromamba
-If you have micromamba on your machine you can prepare environment with just one command: 
+If you are using micromamba you can prepare environment with just one command: 
 
 ```micromamba create --no-channel-priority -c nvidia -c pytorch -c conda-forge -n ammico_env "python=3.10" pytorch torchvision torchaudio pytorch-cuda "tensorflow-gpu<=2.12.3" "numpy<=1.23.4"```  
    

diff --git a/ammico/notebooks/DemoNotebook_ammico.ipynb b/ammico/notebooks/DemoNotebook_ammico.ipynb
diff --git a/ammico/notebooks/colors_analysis.ipynb b/ammico/notebooks/colors_analysis.ipynb
@@ -138,8 +138,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "outdict = ammico.append_data_to_dict(mydict)\n",
-    "df = ammico.dump_df(outdict)"
+    "df = ammico.get_dataframe(mydict)"
    ]
   },
   {

diff --git a/ammico/notebooks/facial_expressions.ipynb b/ammico/notebooks/facial_expressions.ipynb
@@ -136,8 +136,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "outdict = ammico.append_data_to_dict(mydict)\n",
-    "df = ammico.dump_df(outdict)"
+    "df = ammico.get_dataframe(mydict)"
    ]
   },
   {
@@ -177,14 +176,6 @@
    "source": [
     "df.to_csv(\"/content/drive/MyDrive/misinformation-data/data_out.csv\")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b1a80023",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

diff --git a/ammico/notebooks/get-text-from-image.ipynb b/ammico/notebooks/get-text-from-image.ipynb
@@ -164,8 +164,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "outdict = ammico.append_data_to_dict(mydict)\n",
-    "df = ammico.dump_df(outdict)"
+    "df = ammico.get_dataframe(mydict)"
    ]
   },
   {
@@ -339,14 +338,6 @@
    "source": [
     "topic_model.save(\"misinfo_posts\")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7c94edb9",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

diff --git a/ammico/notebooks/image_summary.ipynb b/ammico/notebooks/image_summary.ipynb
@@ -116,7 +116,7 @@
    "outputs": [],
    "source": [
     "for key in mydict:\n",
-    "    mydict[key] = obj.analyse_image(analysis_type=\"summary\", subdict = mydict[key])"
+    "    mydict[key] = obj.analyse_image(subdict = mydict[key], analysis_type=\"summary\")"
    ]
   },
   {
@@ -148,8 +148,7 @@
    },
    "outputs": [],
    "source": [
-    "outdict = ammico.append_data_to_dict(mydict)\n",
-    "df = ammico.dump_df(outdict)"
+    "df = ammico.get_dataframe(mydict)"
    ]
   },
   {
@@ -287,8 +286,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "outdict2 = ammico.append_data_to_dict(mydict)\n",
-    "df2 = ammico.dump_df(outdict2)"
+    "df2 = ammico.get_dataframe(mydict)"
    ]
   },
   {
@@ -510,17 +508,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "outdict = ammico.append_data_to_dict(mydict)\n",
-    "df = ammico.dump_df(outdict)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "mydict"
+    "df = ammico.get_dataframe(mydict)"
    ]
   },
   {

diff --git a/ammico/summary.py b/ammico/summary.py
@@ -239,8 +239,8 @@ def load_vqa_model(self):
 
     def analyse_image(
         self,
-        analysis_type: Optional[str] = None,
         subdict: dict = None,
+        analysis_type: Optional[str] = None,
         list_of_questions: Optional[list[str]] = None,
         consequential_questions: bool = False,
     ):

diff --git a/docs/source/_static/emotion_detector.png b/docs/source/_static/emotion_detector.png
diff --git a/docs/source/_static/summary_detector.png b/docs/source/_static/summary_detector.png
diff --git a/docs/source/_static/text_detector.png b/docs/source/_static/text_detector.png
diff --git a/docs/source/ammico.rst b/docs/source/ammico.rst
@@ -33,23 +33,7 @@ faces module
 color_analysis module
 ---------------------
 
-.. automodule:: color_analysis
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-objects module
---------------
-
-.. automodule:: objects
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-objects_cvlib module
---------------------
-
-.. automodule:: objects_cvlib
+.. automodule:: colors
    :members:
    :undoc-members:
    :show-inheritance:

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -24,6 +24,14 @@
 nbsphinx_allow_errors = True
 napoleon_custom_sections = [("Returns", "params_style")]
 
+html_context = {
+    "display_github": True,  # Integrate GitHub
+    "github_user": "ssciwr",  # Username
+    "github_repo": "AMMICO",  # Repo name
+    "github_version": "main",  # Version
+    "conf_py_path": "/source/",  # Path in the checkout to the docs root
+}
+
 templates_path = ["_templates"]
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -11,12 +11,9 @@ Welcome to AMMICO's documentation!
    :caption: Contents:
 
    readme_link
-   notebooks/Example faces
-   notebooks/Example text
-   notebooks/Example summary
+   notebooks/DemoNotebook_ammico
    notebooks/Example multimodal
    notebooks/Example colors
-   notebooks/Example objects
    notebooks/Example cropposts
    modules
    license_link