# Tracking Changes

## Adding files and the staging area

First let’s make sure we’re still in the right directory. You should be in the planets directory.

pwd

/home/stuart/Git/Aperio/stfc_website/notebooks/02-git



If you are still in moons, navigate back up to planets

pwd

/home/stuart/Git/Aperio/stfc_website/notebooks/02-git


cd ..





Let’s create a file called mars.txt that contains some notes about the Red Planet’s suitability as a base. We’ll use nano to edit the file; you can use whatever editor you like. In particular, this does not have to be the core.editor you set globally earlier. But remember, the bash command to create or edit a new file will depend on the editor you choose (it might not be nano). For a refresher on text editors, check out “Which Editor?” in The Unix Shell lesson.

$nano mars.txt  Type the text below into the mars.txt file: Cold and dry, but everything is my favorite color mars.txt now contains a single line, which we can see by running: ls  00-lessons.ipynb [0m[01;34m02-git[0m [01;34m05-writing-effective-tests[0m [01;34m08-sunpy-and-astropy[0m [01;34m11-tabular-data[0m [01;34m14-searching-and-downloading-data[0m README 00-lessons_instructor.ipynb [01;34m03-fundamentals-of-python[0m [01;34m06-approximating-pi[0m [01;34m09-time-series-data[0m [01;34m12-images-and-visualisation[0m [01;34m15-final-exercise[0m environment.yml [01;34m01-bash[0m [01;34m04-further-python[0m [01;34m07-collaborating-with-git[0m [01;34m10-units[0m [01;34m13-images-in-astronomy[0m LICENCE  cat mars.txt    If we check the status of our project again, Git tells us that it’s noticed the new file: git status  On branch master Your branch is up to date with 'origin/master'. Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) [31mmodified: 02-git/02-creating-repositories_instructor.ipynb[m no changes added to commit (use "git add" and/or "git commit -a")  The “untracked files” message means that there’s a file in the directory that Git isn’t keeping track of. We can tell Git to track a file using git add: git add mars.txt    and then check that the right thing happened: git status  On branch master Your branch is up to date with 'origin/master'. Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) [31mmodified: 02-git/02-creating-repositories_instructor.ipynb[m no changes added to commit (use "git add" and/or "git commit -a")  Git now knows that it’s supposed to keep track of mars.txt, but it hasn’t recorded these changes as a commit yet. To get it to do that, we need to run one more command: git commit -m "Start notes on Mars as a base"  On branch master Your branch is up to date with 'origin/master'. Changes not staged for commit: [31mmodified: 02-git/02-creating-repositories_instructor.ipynb[m no changes added to commit  When we run git commit, Git takes everything we have told it to save by using git add and stores a copy permanently inside the special .git directory. This permanent copy is called a commit (or revision) and its short identifier is f22b25e. Your commit may have another identifier. We use the -m flag (for “message”) to record a short, descriptive, and specific comment that will help us remember later on what we did and why. If we just run git commit without the -m option, Git will launch nano (or whatever other editor we configured as core.editor) so that we can write a longer message. Good commit messages start with a brief (<50 characters) statement about the changes made in the commit. Generally, the message should complete the sentence “If applied, this commit will” . If you want to go into more detail, add a blank line between the summary line and your additional notes. Use this additional space to explain why you made changes and/or what their impact will be. If we run git status now: git status  On branch master Your branch is up to date with 'origin/master'. Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) [31mmodified: 02-git/02-creating-repositories_instructor.ipynb[m no changes added to commit (use "git add" and/or "git commit -a")  it tells us everything is up to date. If we want to know what we’ve done recently, we can ask Git to show us the project’s history using git log: git log  [33mcommit f922c9fa07facba0faa14d2174fcf5c27852eb2a[m[33m ([m[1;36mHEAD -> [m[1;32mmaster[m[33m, [m[1;31morigin/master[m[33m, [m[1;31morigin/HEAD[m[33m)[m Author: Stuart Mumford <stuart@cadair.com> Date: Thu Sep 6 18:15:11 2018 +0100 update notebooks [33mcommit 6053bb89d157b173dda754a895ca3f1076cde97d[m Author: Stuart Mumford <stuart@cadair.com> Date: Thu Sep 6 12:23:57 2018 +0100 update notebooks [33mcommit 51172805ab324552bca7a9427eb966a743b4fada[m Author: Stuart Mumford <stuart@cadair.com> Date: Thu Sep 6 12:03:57 2018 +0100 update notebooks [33mcommit d26b47bc47fa5768ea2073e3b9683c49a6889908[m Author: Stuart Mumford <stuart@cadair.com> Date: Thu Sep 6 11:28:09 2018 +0100 update notebooks [33mcommit 6637293dcb50ae76c9e4a0bf1e2b08dd5a6ce913[m Author: Stuart Mumford <stuart@cadair.com> Date: Thu Sep 6 11:05:50 2018 +0100 update notebooks [33mcommit 35247321b5a0ac13471f18bb4703270d94432b73[m Author: Stuart Mumford <stuart@cadair.com> Date: Wed Sep 5 23:03:45 2018 +0100 update notebooks [33mcommit 58f1a7f5ee4193bcbf72b15979a8f01a1b99a450[m Author: Stuart Mumford <stuart@cadair.com> Date: Wed Sep 5 22:28:02 2018 +0100 update notebooks [33mcommit a967806ebde74eae9d044a895c1651e22e8e0819[m Author: Stuart Mumford <stuart@cadair.com> Date: Wed Sep 5 16:29:44 2018 +0100 update notebooks [33mcommit d47a0802cc1913b5073992f9b6fbcc0b72c86307[m Author: Stuart Mumford <stuart@cadair.com> Date: Wed Sep 5 13:52:51 2018 +0100 add the csv for timeseries [33mcommit 4135ff84e2b4a552317e7087ae14fdbf0093a2eb[m Author: Stuart Mumford <stuart@cadair.com> Date: Wed Sep 5 13:51:07 2018 +0100 update notebooks [33mcommit a9991e8dada1d4de009f1f650a8da84bcfd8757f[m Author: Stuart Mumford <stuart@cadair.com> Date: Tue Sep 4 11:25:33 2018 +0100 update notebooks [33mcommit 5bb6f9a228823fb5890d2c0d6b2e9c0b03673668[m Author: Stuart Mumford <stuart@cadair.com> Date: Tue Sep 4 08:41:44 2018 +0100 update notebooks [33mcommit dd2848367dff52dd13db252e688a085b0638d2c7[m Author: Stuart Mumford <stuart@cadair.com> Date: Mon Sep 3 13:24:05 2018 +0100 update notebooks [33mcommit d3568a1b07b9bf76d89803e610c8ece8d4b94a81[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 19:25:16 2018 +0100 update notebooks [33mcommit f5844e2671a8c7a2b212214a4f6c8bd72428f7c3[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 14:51:57 2018 +0100 rename to avoid website issues [33mcommit ffe8c9dd48510cd2dcbb964c8ead21b93912be21[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 14:43:57 2018 +0100 update notebooks [33mcommit 801632edee8fc310d8500bfaeea8651f099283b3[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 14:43:13 2018 +0100 update notebooks [33mcommit 9c74198bf838b7f7127d8fab527e4d96aab72e08[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 13:46:49 2018 +0100 Add licence and readme to the lessons repo [33mcommit 08b3d7073b526396de7e31ec6e8bd65d075207b6[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 12:59:07 2018 +0100 Add initial dump of rendered lessons  git log lists all commits made to a repository in reverse chronological order. The listing for each commit includes the commit’s full identifier (which starts with the same characters as the short identifier printed by the git commit command earlier), the commit’s author, when it was created, and the log message Git was given when the commit was created. ## # Where Are My Changes? If we run ls at this point, we will still see just one file called mars.txt. That’s because Git saves information about files’ history in the special .git directory mentioned earlier so that our filesystem doesn’t become cluttered (and so that we can’t accidentally edit or delete an old version). Now suppose Dracula adds more information to the file. (Again, we’ll edit with nano and then cat the file to show its contents; you may use a different editor, and don’t need to cat.) nano mars.txt cat mars.txt    Cold and dry, but everything is my favorite color The two moons may be a problem for Wolfman  When we run git status now, it tells us that a file it already knows about has been modified: git status  On branch master Your branch is up to date with 'origin/master'. Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) [31mmodified: 02-git/02-creating-repositories_instructor.ipynb[m no changes added to commit (use "git add" and/or "git commit -a")  The last line is the key phrase: “no changes added to commit”. We have changed this file, but we haven’t told Git we will want to save those changes (which we do with git add) nor have we saved them (which we do with git commit). So let’s do that now. It is good practice to always review our changes before saving them. We do this using git diff. This shows us the differences between the current state of the file and the most recently saved version: git diff  [1mdiff --git a/02-git/02-creating-repositories_instructor.ipynb b/02-git/02-creating-repositories_instructor.ipynb[m [1mindex 0a7156d..4996fde 100644[m [1m--- a/02-git/02-creating-repositories_instructor.ipynb[m [1m+++ b/02-git/02-creating-repositories_instructor.ipynb[m [36m@@ -22,9 +22,32 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 1,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m },[m [32m+[m[32m {[m [32m+[m[32m "name": "stderr",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "/bin/mkdir: cannot create directory ‘planets’: File exists\n"[m [32m+[m[32m ][m [32m+[m[32m },[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "cd ~/Desktop\n",[m "mkdir planets\n",[m [36m@@ -40,9 +63,18 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 2,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "Reinitialized existing Git repository in /home/stuart/Desktop/planets/.git/\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "git init"[m ][m [36m@@ -56,9 +88,17 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 3,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "ls"[m ][m [36m@@ -72,9 +112,18 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 4,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\u001b[0m\u001b[01;34m.\u001b[0m \u001b[01;34m..\u001b[0m \u001b[01;34m.git\u001b[0m\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "ls -a"[m ][m [36m@@ -90,9 +139,22 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 5,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "On branch master\n",[m [32m+[m[32m "\n",[m [32m+[m[32m "No commits yet\n",[m [32m+[m[32m "\n",[m [32m+[m[32m "nothing to commit (create/copy files and use \"git add\" to track)\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "git status"[m ][m  The output is cryptic because it is actually a series of commands for tools like editors and patch telling them how to reconstruct one file given the other. If we break it down into pieces: 1. The first line tells us that Git is producing output similar to the Unix diff command comparing the old and new versions of the file. 2. The second line tells exactly which versions of the file Git is comparing; df0654a and 315bf3a are unique computer-generated labels for those versions. 3. The third and fourth lines once again show the name of the file being changed. 4. The remaining lines are the most interesting, they show us the actual differences and the lines on which they occur. In particular, the + marker in the first column shows where we added a line. After reviewing our change, it’s time to commit it: git commit -m "Add concerns about effects of Mars' moons on Wolfman" git status  On branch master Your branch is up to date with 'origin/master'. Changes not staged for commit: [31mmodified: 02-git/02-creating-repositories_instructor.ipynb[m no changes added to commit On branch master Your branch is up to date with 'origin/master'. Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) [31mmodified: 02-git/02-creating-repositories_instructor.ipynb[m no changes added to commit (use "git add" and/or "git commit -a")  Whoops: Git won’t commit because we didn’t use git add first. Let’s fix that: git add mars.txt git commit -m “Add concerns about effects of Mars’ moons on Wolfman” Git insists that we add files to the set we want to commit before actually committing anything. This allows us to commit our changes in stages and capture changes in logical portions rather than only large batches. For example, suppose we’re adding a few citations to relevant research to our thesis. We might want to commit those additions, and the corresponding bibliography entries, but not commit some of our work drafting the conclusion (which we haven’t finished yet). To allow for this, Git has a special staging area where it keeps track of things that have been added to the current changeset but not yet committed. ## # Staging Area If you think of Git as taking snapshots of changes over the life of a project, git add specifies what will go in a snapshot (putting things in the staging area), and git commit then actually takes the snapshot, and makes a permanent record of it (as a commit). If you don’t have anything staged when you type git commit, Git will prompt you to use git commit -a or git commit --all, which is kind of like gathering everyone for the picture! However, it’s almost always better to explicitly add things to the staging area, because you might commit changes you forgot you made. (Going back to snapshots, you might get the extra with incomplete makeup walking on the stage for the snapshot because you used -a!) Try to stage things manually, or you might find yourself searching for “git undo commit” more than you would like! Let’s watch as our changes to a file move from our editor to the staging area and into long-term storage. First, we’ll add another line to the file: nano mars.txt cat mars.txt    git diff  [1mdiff --git a/02-git/02-creating-repositories_instructor.ipynb b/02-git/02-creating-repositories_instructor.ipynb[m [1mindex 0a7156d..4996fde 100644[m [1m--- a/02-git/02-creating-repositories_instructor.ipynb[m [1m+++ b/02-git/02-creating-repositories_instructor.ipynb[m [36m@@ -22,9 +22,32 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 1,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m },[m [32m+[m[32m {[m [32m+[m[32m "name": "stderr",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "/bin/mkdir: cannot create directory ‘planets’: File exists\n"[m [32m+[m[32m ][m [32m+[m[32m },[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "cd ~/Desktop\n",[m "mkdir planets\n",[m [36m@@ -40,9 +63,18 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 2,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "Reinitialized existing Git repository in /home/stuart/Desktop/planets/.git/\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "git init"[m ][m [36m@@ -56,9 +88,17 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 3,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "ls"[m ][m [36m@@ -72,9 +112,18 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 4,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\u001b[0m\u001b[01;34m.\u001b[0m \u001b[01;34m..\u001b[0m \u001b[01;34m.git\u001b[0m\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "ls -a"[m ][m [36m@@ -90,9 +139,22 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 5,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "On branch master\n",[m [32m+[m[32m "\n",[m [32m+[m[32m "No commits yet\n",[m [32m+[m[32m "\n",[m [32m+[m[32m "nothing to commit (create/copy files and use \"git add\" to track)\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "git status"[m ][m  So far, so good: we’ve added one line to the end of the file (shown with a + in the first column). Now let’s put that change in the staging area and see what git diff reports: git add mars.txt git diff   [1mdiff --git a/02-git/02-creating-repositories_instructor.ipynb b/02-git/02-creating-repositories_instructor.ipynb[m [1mindex 0a7156d..4996fde 100644[m [1m--- a/02-git/02-creating-repositories_instructor.ipynb[m [1m+++ b/02-git/02-creating-repositories_instructor.ipynb[m [36m@@ -22,9 +22,32 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 1,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m },[m [32m+[m[32m {[m [32m+[m[32m "name": "stderr",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "/bin/mkdir: cannot create directory ‘planets’: File exists\n"[m [32m+[m[32m ][m [32m+[m[32m },[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "cd ~/Desktop\n",[m "mkdir planets\n",[m [36m@@ -40,9 +63,18 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 2,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "Reinitialized existing Git repository in /home/stuart/Desktop/planets/.git/\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "git init"[m ][m [36m@@ -56,9 +88,17 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 3,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "ls"[m ][m [36m@@ -72,9 +112,18 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 4,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "\u001b[0m\u001b[01;34m.\u001b[0m \u001b[01;34m..\u001b[0m \u001b[01;34m.git\u001b[0m\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "ls -a"[m ][m [36m@@ -90,9 +139,22 @@[m },[m {[m "cell_type": "code",[m [31m- "execution_count": null,[m [32m+[m[32m "execution_count": 5,[m "metadata": {},[m [31m- "outputs": [],[m [32m+[m[32m "outputs": [[m [32m+[m[32m {[m [32m+[m[32m "name": "stdout",[m [32m+[m[32m "output_type": "stream",[m [32m+[m[32m "text": [[m [32m+[m[32m "On branch master\n",[m [32m+[m[32m "\n",[m [32m+[m[32m "No commits yet\n",[m [32m+[m[32m "\n",[m [32m+[m[32m "nothing to commit (create/copy files and use \"git add\" to track)\n",[m [32m+[m[32m "\n"[m [32m+[m[32m ][m [32m+[m[32m }[m [32m+[m[32m ],[m "source": [[m "git status"[m ][m  There is no output: as far as Git can tell, there’s no difference between what it’s been asked to save permanently and what’s currently in the directory. However, if we do this: git diff --staged    it shows us the difference between the last committed change and what’s in the staging area. Let’s save our changes: git commit -m "Discuss concerns about Mars' climate for Mummy"  On branch master Your branch is up to date with 'origin/master'. Changes not staged for commit: [31mmodified: 02-git/02-creating-repositories_instructor.ipynb[m no changes added to commit  check our status: git status  On branch master Your branch is up to date with 'origin/master'. Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) [31mmodified: 02-git/02-creating-repositories_instructor.ipynb[m no changes added to commit (use "git add" and/or "git commit -a")  and look at the history of what we’ve done so far: git log  [33mcommit f922c9fa07facba0faa14d2174fcf5c27852eb2a[m[33m ([m[1;36mHEAD -> [m[1;32mmaster[m[33m, [m[1;31morigin/master[m[33m, [m[1;31morigin/HEAD[m[33m)[m Author: Stuart Mumford <stuart@cadair.com> Date: Thu Sep 6 18:15:11 2018 +0100 update notebooks [33mcommit 6053bb89d157b173dda754a895ca3f1076cde97d[m Author: Stuart Mumford <stuart@cadair.com> Date: Thu Sep 6 12:23:57 2018 +0100 update notebooks [33mcommit 51172805ab324552bca7a9427eb966a743b4fada[m Author: Stuart Mumford <stuart@cadair.com> Date: Thu Sep 6 12:03:57 2018 +0100 update notebooks [33mcommit d26b47bc47fa5768ea2073e3b9683c49a6889908[m Author: Stuart Mumford <stuart@cadair.com> Date: Thu Sep 6 11:28:09 2018 +0100 update notebooks [33mcommit 6637293dcb50ae76c9e4a0bf1e2b08dd5a6ce913[m Author: Stuart Mumford <stuart@cadair.com> Date: Thu Sep 6 11:05:50 2018 +0100 update notebooks [33mcommit 35247321b5a0ac13471f18bb4703270d94432b73[m Author: Stuart Mumford <stuart@cadair.com> Date: Wed Sep 5 23:03:45 2018 +0100 update notebooks [33mcommit 58f1a7f5ee4193bcbf72b15979a8f01a1b99a450[m Author: Stuart Mumford <stuart@cadair.com> Date: Wed Sep 5 22:28:02 2018 +0100 update notebooks [33mcommit a967806ebde74eae9d044a895c1651e22e8e0819[m Author: Stuart Mumford <stuart@cadair.com> Date: Wed Sep 5 16:29:44 2018 +0100 update notebooks [33mcommit d47a0802cc1913b5073992f9b6fbcc0b72c86307[m Author: Stuart Mumford <stuart@cadair.com> Date: Wed Sep 5 13:52:51 2018 +0100 add the csv for timeseries [33mcommit 4135ff84e2b4a552317e7087ae14fdbf0093a2eb[m Author: Stuart Mumford <stuart@cadair.com> Date: Wed Sep 5 13:51:07 2018 +0100 update notebooks [33mcommit a9991e8dada1d4de009f1f650a8da84bcfd8757f[m Author: Stuart Mumford <stuart@cadair.com> Date: Tue Sep 4 11:25:33 2018 +0100 update notebooks [33mcommit 5bb6f9a228823fb5890d2c0d6b2e9c0b03673668[m Author: Stuart Mumford <stuart@cadair.com> Date: Tue Sep 4 08:41:44 2018 +0100 update notebooks [33mcommit dd2848367dff52dd13db252e688a085b0638d2c7[m Author: Stuart Mumford <stuart@cadair.com> Date: Mon Sep 3 13:24:05 2018 +0100 update notebooks [33mcommit d3568a1b07b9bf76d89803e610c8ece8d4b94a81[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 19:25:16 2018 +0100 update notebooks [33mcommit f5844e2671a8c7a2b212214a4f6c8bd72428f7c3[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 14:51:57 2018 +0100 rename to avoid website issues [33mcommit ffe8c9dd48510cd2dcbb964c8ead21b93912be21[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 14:43:57 2018 +0100 update notebooks [33mcommit 801632edee8fc310d8500bfaeea8651f099283b3[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 14:43:13 2018 +0100 update notebooks [33mcommit 9c74198bf838b7f7127d8fab527e4d96aab72e08[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 13:46:49 2018 +0100 Add licence and readme to the lessons repo [33mcommit 08b3d7073b526396de7e31ec6e8bd65d075207b6[m Author: Stuart Mumford <stuart@cadair.com> Date: Sun Sep 2 12:59:07 2018 +0100 Add initial dump of rendered lessons  ## # Word-based diffing Sometimes, e.g. in the case of the text documents a line-wise diff is too coarse. That is where the --color-words option of git diff comes in very useful as it highlights the changed words using colors. ## # Paging the Log When the output of git log is too long to fit in your screen, git uses a program to split it into pages of the size of your screen. When this “pager” is called, you will notice that the last line in your screen is a :, instead of your usual prompt. • To get out of the pager, press Q. • To move to the next page, press Spacebar. • To search for some_word in all pages, press / and type some_word. Navigate through matches pressing N. ## # Limit Log Size To avoid having git log cover your entire terminal screen, you can limit the number of commits that Git lists by using -N, where N is the number of commits that you want to view. For example, if you only want information from the last commit you can use: $ git log -1

Date:   Thu Aug 22 10:14:07 2013 -0400

Discuss concerns about Mars' climate for Mummy


You can also reduce the quantity of information using the --oneline option:

$git log --oneline * 005937f Discuss concerns about Mars' climate for Mummy * 34961b1 Add concerns about effects of Mars' moons on Wolfman * f22b25e Start notes on Mars as a base  You can also combine the --oneline options with others. One useful combination is: $ git log --oneline --graph --all --decorate

* f22b25e Start notes on Mars as a base


## # Directories

Two important facts you should know about directories in Git.

1. Git does not track directories on their own, only files within them. Try it for yourself:
$mkdir directory$ git status
$git add directory$ git status


Note, our newly created empty directory directory does not appear in the list of untracked files even if we explicitly add it (via git add) to our repository. This is the reason why you will sometimes see .gitkeep files in otherwise empty directories. Unlike .gitignore, these files are not special and their sole purpose is to populate a directory so that Git adds it to the repository. In fact, you can name such files anything you like.

1. If you create a directory in your Git repository and populate it with files, you can add all files in the directory at once by:
git add <directory-with-files>


To recap, when we want to add changes to our repository, we first need to add the changed files to the staging area (git add) and then commit the staged changes to the repository (git commit):

## # Choosing a Commit Message

Which of the following commit messages would be most appropriate for the last commit made to mars.txt?

• “Changes”
• “Added line ‘But the Mummy will appreciate the lack of humidity’ to mars.txt”
• “Discuss effects of Mars’ climate on the Mummy”

## Solution

Answer 1 is not descriptive enough, and the purpose of the commit is unclear; and answer 2 is redundant to using “git diff” to see what changed in this commit; but answer 3 is good: short, descriptive, and imperative.

## # Committing Changes to Git

Which command(s) below would save the changes of myfile.txt to my local Git repository?

$git commit -m "my recent changes"$ git init myfile.txt
$git commit -m "my recent changes"$ git add myfile.txt
$git commit -m "my recent changes"$ git commit -m myfile.txt "my recent changes"


## Solution

• Would only create a commit if files have already been staged.
• Would try to create a new repository.
• Is correct: first add the file to the staging area, then commit.
• Would try to commit a file “my recent changes” with the message myfile.txt.

## # Committing Multiple Files

The staging area can hold changes from any number of files that you want to commit as a single snapshot.

1. Add some text to mars.txt noting your decision to consider Venus as a base
2. Create a new file venus.txt with your initial thoughts about Venus as a base for you and your friends
3. Add changes from both files to the staging area, and commit those changes.

## Solution

First we make our changes to the mars.txt and venus.txt files:

$nano mars.txt$ cat mars.txt

$nano venus.txt$ cat venus.txt

Venus is a nice planet and I definitely should consider it as a base.


Now you can add both files to the staging area. We can do that in one line:

$git add mars.txt venus.txt  Or with multiple commands: $ git add mars.txt
$git add venus.txt  Now the files are ready to commit. You can check that using git status. If you are ready to commit use: $ git commit -m "Write plans to start a base on Venus"

[master cc127c2]
Write plans to start a base on Venus
2 files changed, 2 insertions(+)
create mode 100644 venus.txt


## # bio Repository

• Create a new Git repository on your computer called bio.
• Write a three-line biography for yourself in a file called me.txt, commit your changes
• Modify one line, add a fourth line
• Display the differences between its updated state and its original state.

## Solution

If needed, move out of the planets folder:

$cd ..  Create a new folder called bio and ‘move’ into it: $ mkdir bio
$cd bio  Initialise git: $ git init


Create your biography file me.txt using nano or another text editor. Once in place, add and commit it to the repository:

$git add me.txt$ git commit -m'Adding biography file'


Modify the file as described (modify one line, add a fourth line). To display the differences between its updated state and its original state, use git diff:

$git diff me.txt  ## # Author and Committer For each of the commits you have done, Git stored your name twice. You are named as the author and as the committer. You can observe that by telling Git to show you more information about your last commits: $ git log --format=full


When committing you can name someone else as the author:

$git commit --author="Vlad Dracula <vlad@tran.sylvan.ia>"  Create a new repository and create two commits: one without the --author option and one by naming a colleague of yours as the author. Run git log and git log --format=full. Think about ways how that can allow you to collaborate with your colleagues. ## Solution $ git add me.txt
$git commit -m "Update Vlad's bio." --author="Frank N. Stein <franky@monster.com>" [master 4162a51] Update Vlad's bio. Author: Frank N. Stein <franky@monster.com> 1 file changed, 2 insertions(+), 2 deletions(-)$ git log --format=full
commit 4162a51b273ba799a9d395dd70c45d96dba4e2ff
Author: Frank N. Stein <franky@monster.com>

commit aaa3271e5e26f75f11892718e83a3e2743fab8ea