1st commit

.gitconfig

@@ -0,0 +1,5 @@
+[user]
+	name = ivis-mizuguchi
+	email = rino.mizuguchi@ivis.co.jp
+[http]
+	sslVerify = false

.gitignore

@@ -0,0 +1,13 @@
+
+/.cache/
+/.conda/
+/.config/
+/.ipython/
+/.local/
+/.tmp/
+/.bashrc
+/.bash_logout
+/.profile
+/.netrc
+.ipynb_checkpoints/
+

SECTIONS/enter_metadata.ipynb

@@ -0,0 +1,123 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# 実験メタデータを入力する\n",
+    "\n",
+    "これは、実験日や実験者などのメタデータを入力するためのノートブックです。"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 1. メタデータを入力する"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "1. 以下のセルを実行して、実験日を入力してください。"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "experiment_date = input()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "2. 以下のセルを実行して、実験者を入力してください。"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "experimenter = input()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 2. meta_data.jsonに書き込む"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import json\n",
+    "from collections import OrderedDict\n",
+    "\n",
+    "meta_data = {\n",
+    "    \"experiment_date\": experiment_date,\n",
+    "    \"experimenter\": experimenter\n",
+    "}\n",
+    "with open('../meta_data.json', 'w') as jf:\n",
+    "    json.dump(meta_data, jf, ensure_ascii=False, indent=2)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 3. 変更内容を書き戻す"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%cd ~/\n",
+    "!git add ~/\n",
+    "!git commit -m 'メタデータ入力'\n",
+    "\n",
+    "# import papermill as pm\n",
+    "# \n",
+    "# pm.execute_notebook(\n",
+    "#     './util/datalad_save_push.ipynb',\n",
+    "#     '-',\n",
+    "#     parameters = dict(SAVE_MESSAGE = 'メタデータ入力', PATH = '/home/jovyan/meta_data.json')\n",
+    "# )"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

SECTIONS/finish.ipynb

@@ -0,0 +1,97 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# 実験を終了する\n",
+    "\n",
+    "これは実験を終了するためのノートブックです。"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 1. 実行環境構成を記録する"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%sh\n",
+    "conda env export > ~/environment.yml\n",
+    "pip freeze > ~/requirements.txt"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 2. コミットメッセージを入力する\n",
+    "\n",
+    "以下のセルでコミットメッセージを入力してください。"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "save_message = input()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 3. 実験を書き戻す"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%cd ~/\n",
+    "!git add ~/\n",
+    "!git commit -m $save_message\n",
+    "!git push origin master\n",
+    "\n",
+    "# import papermill as pm\n",
+    "# \n",
+    "# pm.execute_notebook(\n",
+    "#     './util/datalad_save_push.ipynb',\n",
+    "#     '-',\n",
+    "#     parameters = dict(SAVE_MESSAGE = save_message)\n",
+    "# )"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

SECTIONS/save.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# 実験を途中保存する\n",
+    "\n",
+    "これは、実験終了前に実験を途中で保存するためのノートブックです。  \n",
+    "途中保存ではGINリポジトリへの書き戻しは行われませんが、変更履歴が残ります。"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "1. コミットメッセージを変数に入力する"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "save_message = input()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "2. 途中保存する"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%cd ~/\n",
+    "!git add ~/\n",
+    "!git commit -m $save_message\n",
+    "\n",
+    "# from datalad import api\n",
+    "# api.save(message=save_message)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

SECTIONS/util/datalad_save_push.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# ワークフロー実行結果を書き戻す\n",
+    "\n",
+    "このノートブックでは、変更内容をginリポジトリに書き戻します。  \n",
+    "※各セクションのセルでpapermillによって自動実行されるノートブックなので手作業での実施は非推奨です。"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "parameters"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "SIBLING_NAME = \"gin\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "※PATHが指定されない場合は/home/jovyan/をPATHとする"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "parameters"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "PATH = \"/home/jovyan\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 1. 書き戻しの準備を行う"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from datalad import api\n",
+    "\n",
+    "api.save(message=SAVE_MESSAGE, path=PATH, recursive=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 2. 変更内容を書き戻す"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from datalad import api\n",
+    "\n",
+    "api.push(to=SIBLING_NAME, result_renderer='default', path=PATH, recursive=True)"
+   ]
+  }
+ ],
+ "metadata": {
+  "celltoolbar": "Tags",
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

SECTIONS/util/prepare_for_workflow_every_time.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "4719bc46",
+   "metadata": {},
+   "source": [
+    "# ワークフロー実行準備（binder環境起動毎）\n",
+    "\n",
+    "- このノートブックでは、binder環境が起動するたびに必要なワークフロー実行のための処理を行います。"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3d968f7c",
+   "metadata": {},
+   "source": [
+    "## データ書き戻しのための.netrcファイルの設定\n",
+    "\n",
+    "- 以下のセルを実行し、表示されたURLに遷移して、【ユーザ名】と【パスワード】を書き換えてください。"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "178dfe28",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%sh\n",
+    "echo \"\n",
+    "machine dg02.dg.rcos.nii.ac.jp\n",
+    "login 【ユーザ名】\n",
+    "password 【パスワード】\n",
+    "\" > ~/.netrc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ec0051a9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "print(\"https://jupyter.cs.rcos.nii.ac.jp\" + os.environ[\"JUPYTERHUB_SERVICE_PREFIX\"] + \"edit/.netrc\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

experiment.ipynb

@@ -0,0 +1,68 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# 実験支援ノートブック\n",
+    "\n",
+    "これは、実験中のワークフローを支援するためのノートブックです。  \n",
+    "リンクに遷移して必要なワークフローを実行してください。  \n",
+    "※実験は、sourceフォルダ内の [main.ipynb](./source/main.ipynb) に記述してください。"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##  0. 準備"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "|||\n",
+    "|:---:|:---:|\n",
+    "|[書き戻しの準備](./SECTIONS/util/prepare_for_workflow_every_time.ipynb)|"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 1. 実験中ワークフロー"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "||||\n",
+    "|:---:|:---:|:---:|\n",
+    "|[実験メタデータを入力する](./SECTIONS/enter_metadata.ipynb)|[実験を途中保存する](./SECTIONS/save.ipynb)|[実験を終了する](./SECTIONS/finish.ipynb)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

output_data/.gitkeep

@@ -0,0 +1 @@
+

source/main.ipynb

@@ -0,0 +1,32 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}